Variant 11-118005320-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001394165.1(SMIM35):c.*1090A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,060 control chromosomes in the GnomAD database, including 9,891 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 0.31 ( 9891 hom., cov: 32)

Exomes 𝑓: 0.20 ( 0 hom. )

Consequence

SMIM35
NM_001394165.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.325

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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
SMIM35	NM_001394165.1 linkuse as main transcript	c.*1090A>G	3_prime_UTR_variant	5/5	ENST00000689828.1
SMIM35	NM_001394164.1 linkuse as main transcript	c.*1090A>G	3_prime_UTR_variant	6/6
SMIM35	NM_001394166.1 linkuse as main transcript	c.*1090A>G	3_prime_UTR_variant	4/4
SMIM35	XM_024448283.2 linkuse as main transcript	c.*1090A>G	3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMIM35	ENST00000689828.1 linkuse as main transcript	c.*1090A>G		3_prime_UTR_variant	5/5		NM_001394165.1	P1
SMIM35	ENST00000636151.1 linkuse as main transcript	c.*1134A>G		3_prime_UTR_variant	7/7	5		P1

Frequencies

GnomAD3 genomes

AF:

0.308

AC:

46737

AN:

151912

Hom.:

9857

Cov.:

show subpopulations

Gnomad AFR

AF:

0.595

Gnomad AMI

AF:

0.283

Gnomad AMR

AF:

0.231

Gnomad ASJ

AF:

0.248

Gnomad EAS

AF:

0.409

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.293

GnomAD4 exome

AF:

0.200

AC:

AN:

Hom.:

Cov.:

AF XY:

0.167

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 AMR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.167

GnomAD4 genome

AF:

0.308

AC:

46819

AN:

152030

Hom.:

9891

Cov.:

AF XY:

0.308

AC XY:

22874

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.596

Gnomad4 AMR

AF:

0.231

Gnomad4 ASJ

AF:

0.248

Gnomad4 EAS

AF:

0.409

Gnomad4 SAS

AF:

0.231

Gnomad4 FIN

AF:

0.189

Gnomad4 NFE

AF:

0.170

Gnomad4 OTH

AF:

0.293

Alfa

AF:

0.277

Hom.:

1448

Bravo

AF:

0.324

Asia WGS

AF:

0.368

AC:

1278

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

Cadd

Benign

1.6

Dann

Benign

0.38

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