rs12610253

Variant names:

• chr19-7659299-C-G
• rs12610253

Your query was ambiguous. Multiple possible variants found:

• chr19-7659299-C-G
• chr19-7659299-C-T

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 0.315 in 151,852 control chromosomes in the GnomAD database, including 7,572 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 0.32 (7572 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.35 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: 0.315 AC: 47795 AN: 151736 Hom.: 7559 Cov.: 31

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.315 AC: 47848 AN: 151852 Hom.: 7572 Cov.: 31 AF XY: 0.314 AC XY: 23297 AN XY: 74206

African (AFR) AF: 0.311 AC: 12857 AN: 41390

American (AMR) AF: 0.295 AC: 4489 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3466

East Asian (EAS) AF: 0.217 AC: 1122 AN: 5164

South Asian (SAS) AF: 0.364 AC: 1751 AN: 4812

European-Finnish (FIN) AF: 0.355 AC: 3738 AN: 10538

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21778 AN: 67940

Other (OTH) AF: 0.308 AC: 649 AN: 2104

Alfa AF: 0.196 Hom.: 421

Bravo AF: 0.312

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.40
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs12610253; hg19: chr19-7724185;