rs12727642

Variant names:

• chr1-7986612-C-A
• rs12727642

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 0.124 in 152,032 control chromosomes in the GnomAD database, including 1,591 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 0.12 (1591 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 41 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 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: 0.124 AC: 18808 AN: 151914 Hom.: 1589 Cov.: 31

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0629

Gnomad SAS AF: 0.0997

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.124 AC: 18802 AN: 152032 Hom.: 1591 Cov.: 31 AF XY: 0.126 AC XY: 9333 AN XY: 74316

African (AFR) AF: 0.0306 AC: 1270 AN: 41502

American (AMR) AF: 0.100 AC: 1526 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 371 AN: 3468

East Asian (EAS) AF: 0.0627 AC: 324 AN: 5170

South Asian (SAS) AF: 0.0994 AC: 479 AN: 4820

European-Finnish (FIN) AF: 0.283 AC: 2979 AN: 10544

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11547 AN: 67948

Other (OTH) AF: 0.110 AC: 232 AN: 2110

Alfa AF: 0.147 Hom.: 4094

Bravo AF: 0.109

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.4
DANN	Benign	0.47
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs12727642; hg19: chr1-8046672;