19-50431721-G-T

Variant names:

• chr19-50431721-G-T
• rs3810277

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 0.122 in 152,196 control chromosomes in the GnomAD database, including 1,390 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 0.12 (1390 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.40
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18528 AN: 152078 Hom.: 1392 Cov.: 33

Gnomad AFR AF: 0.0558

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0748

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.122 AC: 18530 AN: 152196 Hom.: 1390 Cov.: 33 AF XY: 0.122 AC XY: 9061 AN XY: 74408

African (AFR) AF: 0.0557 AC: 2315 AN: 41538

American (AMR) AF: 0.179 AC: 2733 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3470

East Asian (EAS) AF: 0.140 AC: 720 AN: 5146

South Asian (SAS) AF: 0.196 AC: 944 AN: 4824

European-Finnish (FIN) AF: 0.0748 AC: 794 AN: 10610

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9789 AN: 67994

Other (OTH) AF: 0.145 AC: 307 AN: 2114

Alfa AF: 0.137 Hom.: 2233

Bravo AF: 0.125

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0050
DANN	Benign	0.49
PhyloP100		-5.4

Splicing

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

Other links and lift over

dbSNP: rs3810277; hg19: chr19-50934978;