dbSNP rs17121510: SMIM35:c.*970T>C (chr11-118005440-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001394165.1(SMIM35):c.*970T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,180 control chromosomes in the GnomAD database, including 1,929 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 0.15 ( 1927 hom., cov: 32)

Exomes 𝑓: 0.13 ( 2 hom. )

Consequence

SMIM35
NM_001394165.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.677

Variant links:

Genes affected

SMIM35 (HGNC:44179): (small integral membrane protein 35) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SMIM35 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=-0.69).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
SMIM35	NM_001394165.1 link	c.*970T>C	3_prime_UTR_variant	Exon 5 of 5	ENST00000689828.1	NP_001381094.1
SMIM35	NM_001394164.1 link	c.*970T>C	3_prime_UTR_variant	Exon 6 of 6		NP_001381093.1
SMIM35	NM_001394166.1 link	c.*970T>C	3_prime_UTR_variant	Exon 4 of 4		NP_001381095.1
SMIM35	XM_024448283.2 link	c.*970T>C	3_prime_UTR_variant	Exon 7 of 7		XP_024304051.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM35	ENST00000689828 link	c.*970T>C		3_prime_UTR_variant	Exon 5 of 5		NM_001394165.1	ENSP00000509259.1		A0A1B0GVV1
SMIM35	ENST00000636151 link	c.*1014T>C		3_prime_UTR_variant	Exon 7 of 7	5		ENSP00000490666.1		A0A1B0GVV1

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22110

AN:

151970

Hom.:

1925

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.252

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.0436

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.149

GnomAD4 exome

AF:

0.130

AC:

AN:

Hom.:

Cov.:

AF XY:

0.153

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0946

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.146

AC:

22137

AN:

152088

Hom.:

1927

Cov.:

AF XY:

0.145

AC XY:

10802

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.239

Gnomad4 AMR

AF:

0.120

Gnomad4 ASJ

AF:

0.110

Gnomad4 EAS

AF:

0.0437

Gnomad4 SAS

AF:

0.104

Gnomad4 FIN

AF:

0.117

Gnomad4 NFE

AF:

0.110

Gnomad4 OTH

AF:

0.148

Alfa

AF:

0.119

Hom.:

1725

Bravo

AF:

0.148

Asia WGS

AF:

0.0840

AC:

292

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

4.8

DANN

Benign

0.88

Splicing

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