rs13104811

chr4-74529595-G-Achr4-74529595-G-Cchr4-74529595-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;