rs1268693

Variant names:

• chr12-27974006-A-G
• rs1268693

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 0.623 in 151,706 control chromosomes in the GnomAD database, including 31,748 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 0.62 (31748 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 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: 0.623 AC: 94418 AN: 151588 Hom.: 31695 Cov.: 29

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.623 AC: 94527 AN: 151706 Hom.: 31748 Cov.: 29 AF XY: 0.616 AC XY: 45647 AN XY: 74104

African (AFR) AF: 0.887 AC: 36720 AN: 41396

American (AMR) AF: 0.429 AC: 6536 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1750 AN: 3464

East Asian (EAS) AF: 0.472 AC: 2424 AN: 5132

South Asian (SAS) AF: 0.506 AC: 2423 AN: 4790

European-Finnish (FIN) AF: 0.547 AC: 5741 AN: 10500

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37165 AN: 67864

Other (OTH) AF: 0.564 AC: 1189 AN: 2110

Alfa AF: 0.566 Hom.: 76177

Bravo AF: 0.623

Asia WGS AF: 0.506 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.19
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs1268693; hg19: chr12-28126939;