Variant 11-118004456-C-T 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.*1954G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,898 control chromosomes in the GnomAD database, including 19,620 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 0.51 ( 19613 hom., cov: 31)

Exomes 𝑓: 0.37 ( 7 hom. )

Consequence

SMIM35
NM_001394165.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33

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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
SMIM35	NM_001394165.1 linkuse as main transcript	c.*1954G>A	3_prime_UTR_variant	5/5	ENST00000689828.1	NP_001381094.1
SMIM35	NM_001394164.1 linkuse as main transcript	c.*1954G>A	3_prime_UTR_variant	6/6		NP_001381093.1
SMIM35	NM_001394166.1 linkuse as main transcript	c.*1954G>A	3_prime_UTR_variant	4/4		NP_001381095.1
SMIM35	XM_024448283.2 linkuse as main transcript	c.*1954G>A	3_prime_UTR_variant	7/7		XP_024304051.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMIM35	ENST00000689828.1 linkuse as main transcript	c.*1954G>A		3_prime_UTR_variant	5/5		NM_001394165.1	ENSP00000509259	P1
SMIM35	ENST00000636151.1 linkuse as main transcript	c.*1998G>A		3_prime_UTR_variant	7/7	5		ENSP00000490666	P1

Frequencies

GnomAD3 genomes

AF:

0.507

AC:

76896

AN:

151674

Hom.:

19600

Cov.:

show subpopulations

Gnomad AFR

AF:

0.517

Gnomad AMI

AF:

0.609

Gnomad AMR

AF:

0.577

Gnomad ASJ

AF:

0.510

Gnomad EAS

AF:

0.592

Gnomad SAS

AF:

0.545

Gnomad FIN

AF:

0.408

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.489

Gnomad OTH

AF:

0.536

GnomAD4 exome

AF:

0.368

AC:

AN:

106

Hom.:

Cov.:

AF XY:

0.339

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.348

Gnomad4 NFE exome

AF:

0.542

Gnomad4 OTH exome

AF:

0.214

GnomAD4 genome

AF:

0.507

AC:

76945

AN:

151792

Hom.:

19613

Cov.:

AF XY:

0.508

AC XY:

37673

AN XY:

74174

show subpopulations

Gnomad4 AFR

AF:

0.516

Gnomad4 AMR

AF:

0.577

Gnomad4 ASJ

AF:

0.510

Gnomad4 EAS

AF:

0.592

Gnomad4 SAS

AF:

0.547

Gnomad4 FIN

AF:

0.408

Gnomad4 NFE

AF:

0.489

Gnomad4 OTH

AF:

0.534

Alfa

AF:

0.439

Hom.:

2191

Bravo

AF:

0.520

Asia WGS

AF:

0.583

AC:

2025

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.47

DANN

Benign

0.80

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