dbSNP rs928482: SMIM29:c.137+23C>T (chr6-34247444-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001008703.4(SMIM29):c.137+23C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0588 in 1,571,942 control chromosomes in the GnomAD database, including 8,149 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 0.13 ( 2714 hom., cov: 32)

Exomes 𝑓: 0.051 ( 5435 hom. )

Consequence

SMIM29
NM_001008703.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05

Publications

5 publications found

Variant links:

Genes affected

SMIM29 (HGNC:1340): (small integral membrane protein 29) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SMIM29 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMIM29	NM_001008703.4 link	c.137+23C>T		intron_variant	Intron 3 of 4	ENST00000476320.6	NP_001008703.2	Q86T20-1A0A2U3TZT1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM29	ENST00000476320.6 link	c.137+23C>T		intron_variant	Intron 3 of 4	2	NM_001008703.4	ENSP00000417604.2		Q86T20-1

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20335

AN:

151960

Hom.:

2696

Cov.:

show subpopulations

Gnomad AFR

AF:

0.318

Gnomad AMI

AF:

0.0800

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.0570

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.0409

Gnomad FIN

AF:

0.0168

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0325

Gnomad OTH

AF:

0.132

GnomAD2 exomes

AF:

0.108

AC:

20247

AN:

186898

AF XY:

0.0930

show subpopulations

Gnomad AFR exome

AF:

0.348

Gnomad AMR exome

AF:

0.338

Gnomad ASJ exome

AF:

0.0486

Gnomad EAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.0210

Gnomad NFE exome

AF:

0.0355

Gnomad OTH exome

AF:

0.0863

GnomAD4 exome

AF:

0.0507

AC:

71970

AN:

1419864

Hom.:

5435

Cov.:

AF XY:

0.0490

AC XY:

34380

AN XY:

701984

show subpopulations

African (AFR)

AF:

0.325

AC:

10732

AN:

33050

American (AMR)

AF:

0.319

AC:

12306

AN:

38532

Ashkenazi Jewish (ASJ)

AF:

0.0493

AC:

1246

AN:

25256

East Asian (EAS)

AF:

0.162

AC:

6190

AN:

38240

South Asian (SAS)

AF:

0.0403

AC:

3246

AN:

80574

European-Finnish (FIN)

AF:

0.0199

AC:

1002

AN:

50352

Middle Eastern (MID)

AF:

0.0960

AC:

548

AN:

5706

European-Non Finnish (NFE)

AF:

0.0301

AC:

32798

AN:

1089338

Other (OTH)

AF:

0.0663

AC:

3902

AN:

58816

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.566

Heterozygous variant carriers

3009

6018

9027

12036

15045

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1552

3104

4656

6208

7760

<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:

0.134

AC:

20397

AN:

152078

Hom.:

2714

Cov.:

AF XY:

0.133

AC XY:

9901

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.318

AC:

13169

AN:

41402

American (AMR)

AF:

0.225

AC:

3428

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0570

AC:

198

AN:

3472

East Asian (EAS)

AF:

0.124

AC:

643

AN:

5166

South Asian (SAS)

AF:

0.0406

AC:

196

AN:

4832

European-Finnish (FIN)

AF:

0.0168

AC:

178

AN:

10618

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0325

AC:

2208

AN:

68002

Other (OTH)

AF:

0.131

AC:

277

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.558

Heterozygous variant carriers

696

1392

2088

2784

3480

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.0580

Hom.:

312

Bravo

AF:

0.162

Asia WGS

AF:

0.0980

AC:

340

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.11

(source)

DANN

Benign

0.48

PhyloP100

-1.1

Mutation Taster

=14/86

disease causing

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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