rs3760722

Variant names:

• chr19-50854560-C-T
• rs3760722

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 0.141 in 152,046 control chromosomes in the GnomAD database, including 2,068 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 0.14 (2068 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 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: 0.141 AC: 21470 AN: 151928 Hom.: 2062 Cov.: 31

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0746

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.0481

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0972

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.141 AC: 21498 AN: 152046 Hom.: 2068 Cov.: 31 AF XY: 0.138 AC XY: 10236 AN XY: 74358

African (AFR) AF: 0.271 AC: 11235 AN: 41406

American (AMR) AF: 0.110 AC: 1677 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3472

East Asian (EAS) AF: 0.0747 AC: 386 AN: 5164

South Asian (SAS) AF: 0.0483 AC: 233 AN: 4826

European-Finnish (FIN) AF: 0.0481 AC: 510 AN: 10610

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0972 AC: 6607 AN: 67978

Other (OTH) AF: 0.143 AC: 301 AN: 2106

Alfa AF: 0.111 Hom.: 1884

Bravo AF: 0.155

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.66
DANN	Benign	0.45
PhyloP100		-1.2
PromoterAI		0.0054	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3760722; hg19: chr19-51357816;