chr3-51721096-T-A

Variant names:

• chr3-51721096-T-A
• rs4687771

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 0.223 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.324 AC: 13394 AN: 41344

American (AMR) AF: 0.355 AC: 5421 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3466

East Asian (EAS) AF: 0.387 AC: 1989 AN: 5140

South Asian (SAS) AF: 0.168 AC: 805 AN: 4794

European-Finnish (FIN) AF: 0.154 AC: 1629 AN: 10562

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9476 AN: 67942

Other (OTH) AF: 0.195 AC: 410 AN: 2106

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
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs4687771; hg19: chr3-51755112;