rs3760721

Variant names:

• chr19-50854248-C-T
• rs3760721

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 0.229 in 152,036 control chromosomes in the GnomAD database, including 4,785 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 0.23 (4785 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 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: 0.229 AC: 34824 AN: 151918 Hom.: 4779 Cov.: 30

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.229 AC: 34843 AN: 152036 Hom.: 4785 Cov.: 30 AF XY: 0.232 AC XY: 17229 AN XY: 74304

African (AFR) AF: 0.0886 AC: 3677 AN: 41496

American (AMR) AF: 0.327 AC: 4997 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 800 AN: 3468

East Asian (EAS) AF: 0.352 AC: 1813 AN: 5154

South Asian (SAS) AF: 0.166 AC: 799 AN: 4820

European-Finnish (FIN) AF: 0.350 AC: 3691 AN: 10548

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.270 AC: 18321 AN: 67966

Other (OTH) AF: 0.221 AC: 463 AN: 2098

Alfa AF: 0.261 Hom.: 2110

Bravo AF: 0.222

Asia WGS AF: 0.262 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.55
DANN	Benign	0.56
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs3760721; hg19: chr19-51357504;