dbSNP rs2301682: CFAP97D1:c.124+72G>T (chr17-43780658-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001136483.3(CFAP97D1):c.124+72G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0834 in 1,513,158 control chromosomes in the GnomAD database, including 5,799 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 0.10 ( 979 hom., cov: 32)

Exomes 𝑓: 0.081 ( 4820 hom. )

Consequence

CFAP97D1
NM_001136483.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.15

Publications

9 publications found

Variant links:

Genes affected

CFAP97D1 (HGNC:37241): (CFAP97 domain containing 1) Predicted to be involved in sperm axoneme assembly. [provided by Alliance of Genome Resources, Apr 2022]

CFAP97D1 links:

Genome browser will be placed here

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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP97D1	NM_001136483.3 link	c.124+72G>T		intron_variant	Intron 1 of 5	ENST00000449302.8	NP_001129955.1	B2RV13
CFAP97D1	NM_001353400.2 link	c.124+72G>T		intron_variant	Intron 1 of 4		NP_001340329.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP97D1	ENST00000449302.8 link	c.124+72G>T		intron_variant	Intron 1 of 5	1	NM_001136483.3	ENSP00000415662.2		B2RV13

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15419

AN:

152114

Hom.:

975

Cov.:

show subpopulations

Gnomad AFR

AF:

0.169

Gnomad AMI

AF:

0.0625

Gnomad AMR

AF:

0.0776

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.137

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.0269

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.0737

Gnomad OTH

AF:

0.108

GnomAD4 exome

AF:

0.0814

AC:

110776

AN:

1360926

Hom.:

4820

AF XY:

0.0824

AC XY:

55370

AN XY:

671972

show subpopulations

African (AFR)

AF:

0.182

AC:

5573

AN:

30612

American (AMR)

AF:

0.0742

AC:

2588

AN:

34860

Ashkenazi Jewish (ASJ)

AF:

0.0902

AC:

2203

AN:

24412

East Asian (EAS)

AF:

0.125

AC:

4418

AN:

35458

South Asian (SAS)

AF:

0.114

AC:

8787

AN:

77228

European-Finnish (FIN)

AF:

0.0343

AC:

1640

AN:

47822

Middle Eastern (MID)

AF:

0.155

AC:

866

AN:

5604

European-Non Finnish (NFE)

AF:

0.0756

AC:

79235

AN:

1048288

Other (OTH)

AF:

0.0965

AC:

5466

AN:

56642

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

4831

9661

14492

19322

24153

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3120

6240

9360

12480

15600

<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:

0.101

AC:

15434

AN:

152232

Hom.:

979

Cov.:

AF XY:

0.0986

AC XY:

7336

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.169

AC:

7000

AN:

41522

American (AMR)

AF:

0.0784

AC:

1200

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.103

AC:

356

AN:

3470

East Asian (EAS)

AF:

0.137

AC:

709

AN:

5182

South Asian (SAS)

AF:

0.113

AC:

543

AN:

4824

European-Finnish (FIN)

AF:

0.0269

AC:

285

AN:

10610

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0738

AC:

5017

AN:

68006

Other (OTH)

AF:

0.106

AC:

225

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

681

1362

2044

2725

3406

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.0881

Hom.:

457

Bravo

AF:

0.111

Asia WGS

AF:

0.129

AC:

447

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.050

(source)

DANN

Benign

0.69

PhyloP100

-2.1

PromoterAI

-0.078

Neutral

(source)

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over