Genetic Variant SAPCD1:c.114+69C>G (chr6-31763237-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001039651.2(SAPCD1):c.114+69C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,201,240 control chromosomes in the GnomAD database, including 32,610 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.26 ( 5661 hom., cov: 32)

Exomes 𝑓: 0.22 ( 26949 hom. )

Consequence

SAPCD1
NM_001039651.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.308

Publications

27 publications found

Variant links:

Genes affected

SAPCD1 (HGNC:13938): (suppressor APC domain containing 1)

SAPCD1 links:

MSH5-SAPCD1 (HGNC:41994): (MSH5-SAPCD1 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring mutS homolog 5 (MSH5) and chromosome 6 open reading frame 26 (C6orf26) genes. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]

MSH5-SAPCD1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039651.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAPCD1	NM_001039651.2	MANE Select	c.114+69C>G		intron	N/A	NP_001034740.1
	MSH5-SAPCD1	NR_037846.1		n.3321+69C>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SAPCD1	ENST00000415669.4	TSL:1 MANE Select	c.114+69C>G	intron	N/A	ENSP00000411948.2
MSH5-SAPCD1	ENST00000493662.6	TSL:1	n.*637+69C>G	intron	N/A	ENSP00000417871.2
MSH5-SAPCD1	ENST00000498473.6	TSL:1	n.*681+69C>G	intron	N/A	ENSP00000419220.2

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

39425

AN:

151994

Hom.:

5657

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.347

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.475

Gnomad SAS

AF:

0.271

Gnomad FIN

AF:

0.204

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.264

GnomAD4 exome

AF:

0.217

AC:

227765

AN:

1049128

Hom.:

26949

Cov.:

AF XY:

0.217

AC XY:

114754

AN XY:

528438

show subpopulations

African (AFR)

AF:

0.332

AC:

8007

AN:

24146

American (AMR)

AF:

0.348

AC:

10076

AN:

28988

Ashkenazi Jewish (ASJ)

AF:

0.136

AC:

2724

AN:

20068

East Asian (EAS)

AF:

0.430

AC:

14834

AN:

34510

South Asian (SAS)

AF:

0.271

AC:

18337

AN:

67620

European-Finnish (FIN)

AF:

0.202

AC:

9616

AN:

47518

Middle Eastern (MID)

AF:

0.185

AC:

891

AN:

4810

European-Non Finnish (NFE)

AF:

0.197

AC:

153038

AN:

775246

Other (OTH)

AF:

0.222

AC:

10242

AN:

46222

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

9788

19575

29363

39150

48938

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5022

10044

15066

20088

25110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.259

AC:

39463

AN:

152112

Hom.:

5661

Cov.:

AF XY:

0.263

AC XY:

19566

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.330

AC:

13687

AN:

41484

American (AMR)

AF:

0.348

AC:

5316

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.134

AC:

464

AN:

3472

East Asian (EAS)

AF:

0.475

AC:

2453

AN:

5166

South Asian (SAS)

AF:

0.271

AC:

1306

AN:

4822

European-Finnish (FIN)

AF:

0.204

AC:

2154

AN:

10580

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.197

AC:

13378

AN:

67992

Other (OTH)

AF:

0.263

AC:

555

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1475

2950

4425

5900

7375

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

408

816

1224

1632

2040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.217

Hom.:

516

Bravo

AF:

0.273

Asia WGS

AF:

0.301

AC:

1045

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.1

(source)

DANN

Benign

0.53

PhyloP100

0.31

PromoterAI

0.0046

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over