rs4687771

Positions:

• chr3-51721096-T-A
• chr3-51721096-T-G

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 0.223 in 151,824 control chromosomes in the GnomAD database, including 4,610 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 0.22 (4610 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.925

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33750 AN: 151704 Hom.: 4588 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.223 AC: 33818 AN: 151824 Hom.: 4610 Cov.: 32 AF XY: 0.226 AC XY: 16746 AN XY: 74188

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.195

Alfa AF: 0.178 Hom.: 391

Bravo AF: 0.244

Asia WGS AF: 0.265 AC: 924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4687771; hg19: chr3-51755112;