11-73997476-C-T

Variant names:

• chr11-73997476-C-T
• rs590336
• ENST00000756716.1:n.492+1442C>T

Variant summary

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

The ENST00000756716.1(ENSG00000298594):​n.492+1442C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,936 control chromosomes in the GnomAD database, including 24,275 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 0.56 (24275 hom., cov: 30)
• Consequence: ENSG00000298594 ENST00000756716.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01
• Publications: 14 publications found

Genes affected

ENSG00000298594 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298594	ENST00000756716.1	n.492+1442C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85401 AN: 151814 Hom.: 24264 Cov.: 30

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.562 AC: 85459 AN: 151936 Hom.: 24275 Cov.: 30 AF XY: 0.564 AC XY: 41872 AN XY: 74286

African (AFR) AF: 0.664 AC: 27501 AN: 41424

American (AMR) AF: 0.528 AC: 8053 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1839 AN: 3460

East Asian (EAS) AF: 0.438 AC: 2263 AN: 5162

South Asian (SAS) AF: 0.499 AC: 2403 AN: 4818

European-Finnish (FIN) AF: 0.598 AC: 6319 AN: 10566

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35418 AN: 67930

Other (OTH) AF: 0.529 AC: 1117 AN: 2110

Alfa AF: 0.526 Hom.: 55572

Bravo AF: 0.561

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.18
DANN	Benign	0.39
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs590336; hg19: chr11-73708521; COSMIC: COSV58367524;