chr19-50900964-A-T

Variant names:

• chr19-50900964-A-T
• rs1701941

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 0.42 in 151,876 control chromosomes in the GnomAD database, including 14,344 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 0.42 (14344 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 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: 0.421 AC: 63817 AN: 151760 Hom.: 14339 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.0515

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.420 AC: 63855 AN: 151876 Hom.: 14344 Cov.: 32 AF XY: 0.421 AC XY: 31213 AN XY: 74216

African (AFR) AF: 0.302 AC: 12480 AN: 41382

American (AMR) AF: 0.464 AC: 7079 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1847 AN: 3468

East Asian (EAS) AF: 0.0521 AC: 269 AN: 5168

South Asian (SAS) AF: 0.323 AC: 1551 AN: 4804

European-Finnish (FIN) AF: 0.528 AC: 5571 AN: 10556

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.493 AC: 33518 AN: 67920

Other (OTH) AF: 0.435 AC: 917 AN: 2110

Alfa AF: 0.459 Hom.: 2053

Bravo AF: 0.409

Asia WGS AF: 0.193 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.16
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1701941; hg19: chr19-51404220;