Variant rs1150780 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001008703.4(SMIM29):c.137+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,573,726 control chromosomes in the GnomAD database, including 46,268 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 0.18 ( 3186 hom., cov: 32)

Exomes 𝑓: 0.24 ( 43082 hom. )

Consequence

SMIM29
NM_001008703.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.103

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMIM29	NM_001008703.4 linkuse as main transcript	c.137+16C>T		intron_variant		ENST00000476320.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMIM29	ENST00000476320.6 linkuse as main transcript	c.137+16C>T		intron_variant		2	NM_001008703.4	P1	Q86T20-1

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27514

AN:

151772

Hom.:

3184

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0474

Gnomad AMI

AF:

0.106

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.123

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.221

Gnomad FIN

AF:

0.311

Gnomad MID

AF:

0.162

Gnomad NFE

AF:

0.243

Gnomad OTH

AF:

0.155

GnomAD3 exomes

AF:

0.214

AC:

40545

AN:

189788

Hom.:

4777

AF XY:

0.218

AC XY:

21996

AN XY:

100712

show subpopulations

Gnomad AFR exome

AF:

0.0377

Gnomad AMR exome

AF:

0.167

Gnomad ASJ exome

AF:

0.130

Gnomad EAS exome

AF:

0.254

Gnomad SAS exome

AF:

0.233

Gnomad FIN exome

AF:

0.298

Gnomad NFE exome

AF:

0.236

Gnomad OTH exome

AF:

0.199

GnomAD4 exome

AF:

0.241

AC:

342752

AN:

1421834

Hom.:

43082

Cov.:

AF XY:

0.240

AC XY:

169085

AN XY:

703070

show subpopulations

Gnomad4 AFR exome

AF:

0.0358

Gnomad4 AMR exome

AF:

0.170

Gnomad4 ASJ exome

AF:

0.130

Gnomad4 EAS exome

AF:

0.229

Gnomad4 SAS exome

AF:

0.231

Gnomad4 FIN exome

AF:

0.295

Gnomad4 NFE exome

AF:

0.253

Gnomad4 OTH exome

AF:

0.224

GnomAD4 genome

AF:

0.181

AC:

27517

AN:

151892

Hom.:

3186

Cov.:

AF XY:

0.183

AC XY:

13597

AN XY:

74196

show subpopulations

Gnomad4 AFR

AF:

0.0473

Gnomad4 AMR

AF:

0.167

Gnomad4 ASJ

AF:

0.123

Gnomad4 EAS

AF:

0.250

Gnomad4 SAS

AF:

0.222

Gnomad4 FIN

AF:

0.311

Gnomad4 NFE

AF:

0.243

Gnomad4 OTH

AF:

0.162

Alfa

AF:

0.213

Hom.:

1443

Bravo

AF:

0.164

Asia WGS

AF:

0.253

AC:

881

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.6

DANN

Benign

0.73

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over