19-50920372-T-G

Variant names:

• chr19-50920372-T-G
• rs8101572

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 0.525 in 151,954 control chromosomes in the GnomAD database, including 22,693 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 0.53 (22693 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79702 AN: 151836 Hom.: 22658 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.525 AC: 79786 AN: 151954 Hom.: 22693 Cov.: 31 AF XY: 0.525 AC XY: 38968 AN XY: 74258

African (AFR) AF: 0.720 AC: 29843 AN: 41468

American (AMR) AF: 0.422 AC: 6437 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1217 AN: 3468

East Asian (EAS) AF: 0.906 AC: 4682 AN: 5166

South Asian (SAS) AF: 0.583 AC: 2811 AN: 4824

European-Finnish (FIN) AF: 0.414 AC: 4356 AN: 10522

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28885 AN: 67948

Other (OTH) AF: 0.489 AC: 1031 AN: 2110

Alfa AF: 0.462 Hom.: 59084

Bravo AF: 0.535

Asia WGS AF: 0.716 AC: 2487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.56
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs8101572; hg19: chr19-51423628;