19-21010275-C-T

Variant names:

• chr19-21010275-C-T
• rs12608931

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;