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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.548

Alfa AF: 0.573 Hom.: 16574

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13104811; hg19: chr4-75395312;