ENST00000634657.2:n.336+1872C>A

Variant names:

• chr11-92917836-C-A
• rs7950811
• ENST00000634657.2:n.336+1872C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634657.2(ENSG00000290774):​n.336+1872C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 152,086 control chromosomes in the GnomAD database, including 419 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 0.068 (419 hom., cov: 33)
• Consequence: ENSG00000290774 ENST00000634657.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 19 publications found

Genes affected

ENSG00000290774 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634657.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290774	ENST00000634657.2	TSL:5	n.336+1872C>A		intron	N/A
	ENSG00000290774	ENST00000749913.1		n.257+1872C>A		intron	N/A
	ENSG00000290774	ENST00000749914.1		n.244+1872C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0681 AC: 10345 AN: 151968 Hom.: 416 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.0704

Gnomad SAS AF: 0.0415

Gnomad FIN AF: 0.0434

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0424

Gnomad OTH AF: 0.0686

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

GnomAD4 genome AF: 0.0682 AC: 10368 AN: 152086 Hom.: 419 Cov.: 33 AF XY: 0.0674 AC XY: 5012 AN XY: 74352

African (AFR) AF: 0.116 AC: 4814 AN: 41464

American (AMR) AF: 0.0778 AC: 1189 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3470

East Asian (EAS) AF: 0.0709 AC: 367 AN: 5176

South Asian (SAS) AF: 0.0414 AC: 199 AN: 4810

European-Finnish (FIN) AF: 0.0434 AC: 459 AN: 10578

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0424 AC: 2882 AN: 67986

Other (OTH) AF: 0.0688 AC: 145 AN: 2108

Alfa AF: 0.0498 Hom.: 991

Bravo AF: 0.0723

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.34
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs7950811; hg19: chr11-92651002;