19-21010275-C-T

Position:

• chr19-21010275-C-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 0.683 in 152,036 control chromosomes in the GnomAD database, including 39,630 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 0.68 (39630 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103861 AN: 151920 Hom.: 39637 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.683 AC: 103866 AN: 152036 Hom.: 39630 Cov.: 32 AF XY: 0.686 AC XY: 50979 AN XY: 74298

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.739

Alfa AF: 0.752 Hom.: 5686

Bravo AF: 0.668

Asia WGS AF: 0.760 AC: 2643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12608931; hg19: chr19-21193081;