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. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.630 AC: 26128 AN: 41450

American (AMR) AF: 0.866 AC: 13244 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2701 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5149 AN: 5154

South Asian (SAS) AF: 0.826 AC: 3985 AN: 4826

European-Finnish (FIN) AF: 0.874 AC: 9266 AN: 10602

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58940 AN: 68034

Other (OTH) AF: 0.799 AC: 1687 AN: 2112

Alfa AF: 0.829 Hom.: 18793

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4771633; hg19: chr13-110060787;