11-118024067-A-T

Variant names:

• chr11-118024067-A-T
• rs11216700
• NM_001394165.1:c.8-8258T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394165.1(SMIM35):​c.8-8258T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0566 in 151,954 control chromosomes in the GnomAD database, including 542 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 0.057 (542 hom., cov: 31)
• Consequence: SMIM35 NM_001394165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMIM35	NM_001394165.1	c.8-8258T>A		intron_variant	Intron 1 of 4	ENST00000689828.1	NP_001381094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM35	ENST00000689828.1	c.8-8258T>A		intron_variant	Intron 1 of 4		NM_001394165.1	ENSP00000509259.1

Frequencies

GnomAD3 genomes AF: 0.0567 AC: 8604 AN: 151840 Hom.: 542 Cov.: 31

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0568

Gnomad OTH AF: 0.0578

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0566 AC: 8602 AN: 151954 Hom.: 542 Cov.: 31 AF XY: 0.0595 AC XY: 4420 AN XY: 74240

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0537

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0587

Gnomad4 NFE AF: 0.0568

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0529 Hom.: 37

Bravo AF: 0.0546

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.8
DANN	Benign	0.22

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11216700; hg19: chr11-117894782;