19-50900964-A-T

Position:

• chr19-50900964-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.0521

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.435

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1701941; hg19: chr19-51404220;