rs4771450

Variant names:

• chr13-103317141-G-A
• rs4771450

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 0.652 in 151,992 control chromosomes in the GnomAD database, including 32,561 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 0.65 (32561 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.852

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 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: 0.652 AC: 98968 AN: 151872 Hom.: 32537 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.652 AC: 99045 AN: 151992 Hom.: 32561 Cov.: 32 AF XY: 0.647 AC XY: 48060 AN XY: 74266

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.647

Alfa AF: 0.638 Hom.: 9136

Bravo AF: 0.656

Asia WGS AF: 0.606 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4771450; hg19: chr13-103969491;