19-39773326-C-T

Variant names:

• chr19-39773326-C-T
• rs10412191

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 0.712 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.894

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.703

Alfa AF: 0.652 Hom.: 46218

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10412191; hg19: chr19-40263966;