rs13104811

Variant names:

• chr4-74529595-G-A
• rs13104811

Your query was ambiguous. Multiple possible variants found:

• chr4-74529595-G-A
• chr4-74529595-G-C
• chr4-74529595-G-T

Variant summary

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

The variant allele was found at a frequency of 0.543 in 151,948 control chromosomes in the GnomAD database, including 23,247 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 0.54 (23247 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 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

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82465 AN: 151830 Hom.: 23250 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.543 AC: 82476 AN: 151948 Hom.: 23247 Cov.: 32 AF XY: 0.546 AC XY: 40522 AN XY: 74228

African (AFR) AF: 0.384 AC: 15901 AN: 41428

American (AMR) AF: 0.628 AC: 9582 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1693 AN: 3466

East Asian (EAS) AF: 0.634 AC: 3263 AN: 5150

South Asian (SAS) AF: 0.566 AC: 2723 AN: 4808

European-Finnish (FIN) AF: 0.659 AC: 6962 AN: 10572

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40663 AN: 67960

Other (OTH) AF: 0.548 AC: 1158 AN: 2114

Alfa AF: 0.571 Hom.: 58134

Bravo AF: 0.539

Asia WGS AF: 0.578 AC: 2013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.72
DANN	Benign	0.25
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs13104811; hg19: chr4-75395312;