19-56080920-C-T

Variant names:

• chr19-56080920-C-T
• rs6509981

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 0.591 in 152,204 control chromosomes in the GnomAD database, including 26,767 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 0.59 (26767 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 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: 0.591 AC: 89883 AN: 152088 Hom.: 26738 Cov.: 34

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.591 AC: 89973 AN: 152204 Hom.: 26767 Cov.: 34 AF XY: 0.595 AC XY: 44252 AN XY: 74402

African (AFR) AF: 0.543 AC: 22548 AN: 41540

American (AMR) AF: 0.560 AC: 8564 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2078 AN: 3472

East Asian (EAS) AF: 0.612 AC: 3156 AN: 5158

South Asian (SAS) AF: 0.624 AC: 3015 AN: 4828

European-Finnish (FIN) AF: 0.701 AC: 7420 AN: 10592

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.609 AC: 41417 AN: 67996

Other (OTH) AF: 0.551 AC: 1165 AN: 2114

Alfa AF: 0.592 Hom.: 40575

Bravo AF: 0.578

Asia WGS AF: 0.622 AC: 2164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.7
DANN	Benign	0.90
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs6509981; hg19: chr19-56592286;