19-39773326-C-T

Variant names:

• chr19-39773326-C-T
• rs10412191

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 0.712 in 151,774 control chromosomes in the GnomAD database, including 39,676 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 0.71 (39676 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 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: 0.712 AC: 107980 AN: 151652 Hom.: 39607 Cov.: 29

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.712 AC: 108105 AN: 151774 Hom.: 39676 Cov.: 29 AF XY: 0.713 AC XY: 52872 AN XY: 74164

African (AFR) AF: 0.894 AC: 37028 AN: 41436

American (AMR) AF: 0.704 AC: 10724 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2367 AN: 3464

East Asian (EAS) AF: 0.529 AC: 2722 AN: 5142

South Asian (SAS) AF: 0.575 AC: 2762 AN: 4806

European-Finnish (FIN) AF: 0.685 AC: 7200 AN: 10512

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.636 AC: 43183 AN: 67870

Other (OTH) AF: 0.703 AC: 1481 AN: 2106

Alfa AF: 0.663 Hom.: 126350

Bravo AF: 0.720

Asia WGS AF: 0.602 AC: 2095 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10412191; hg19: chr19-40263966;