rs4771633

Variant names:

• chr13-109408440-G-A
• rs4771633

Your query was ambiguous. Multiple possible variants found:

• chr13-109408440-G-A
• chr13-109408440-G-C
• chr13-109408440-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 0.803 in 152,148 control chromosomes in the GnomAD database, including 49,969 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 0.80 (49969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.803 AC: 122091 AN: 152030 Hom.: 49934 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.803 AC: 122176 AN: 152148 Hom.: 49969 Cov.: 32 AF XY: 0.805 AC XY: 59874 AN XY: 74382

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.799

Alfa AF: 0.817 Hom.: 9503

Bravo AF: 0.798

Asia WGS AF: 0.915 AC: 3184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4771633; hg19: chr13-110060787;