19-21010275-C-T

Variant names:

• chr19-21010275-C-T
• rs12608931

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 0.683 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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

African (AFR) AF: 0.315 AC: 13047 AN: 41434

American (AMR) AF: 0.779 AC: 11910 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3087 AN: 3470

East Asian (EAS) AF: 0.856 AC: 4411 AN: 5154

South Asian (SAS) AF: 0.782 AC: 3774 AN: 4828

European-Finnish (FIN) AF: 0.766 AC: 8085 AN: 10554

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 57013 AN: 67998

Other (OTH) AF: 0.739 AC: 1560 AN: 2110

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

Other links and lift over

dbSNP: rs12608931; hg19: chr19-21193081;