19-40990556-T-C

Variant names:

• chr19-40990556-T-C
• rs4802101

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 0.698 in 151,420 control chromosomes in the GnomAD database, including 38,381 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 0.70 (38381 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105547 AN: 151302 Hom.: 38331 Cov.: 28

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.698 AC: 105656 AN: 151420 Hom.: 38381 Cov.: 28 AF XY: 0.700 AC XY: 51735 AN XY: 73918

African (AFR) AF: 0.901 AC: 37099 AN: 41192

American (AMR) AF: 0.759 AC: 11549 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2124 AN: 3466

East Asian (EAS) AF: 0.657 AC: 3380 AN: 5146

South Asian (SAS) AF: 0.753 AC: 3603 AN: 4784

European-Finnish (FIN) AF: 0.586 AC: 6129 AN: 10466

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39714 AN: 67856

Other (OTH) AF: 0.689 AC: 1446 AN: 2100

Alfa AF: 0.656 Hom.: 4434

Bravo AF: 0.717

Asia WGS AF: 0.713 AC: 2476 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4802101; hg19: chr19-41496461;