rs12746613

Variant names:

• chr1-161497252-C-T
• rs12746613

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 0.0884 in 152,172 control chromosomes in the GnomAD database, including 857 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 0.088 (857 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 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: 0.0885 AC: 13452 AN: 152054 Hom.: 857 Cov.: 32

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0853

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0884 AC: 13446 AN: 152172 Hom.: 857 Cov.: 32 AF XY: 0.0890 AC XY: 6623 AN XY: 74386

African (AFR) AF: 0.0202 AC: 840 AN: 41548

American (AMR) AF: 0.0989 AC: 1512 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 879 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0853 AC: 411 AN: 4816

European-Finnish (FIN) AF: 0.111 AC: 1172 AN: 10572

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.122 AC: 8304 AN: 67978

Other (OTH) AF: 0.0994 AC: 210 AN: 2112

Alfa AF: 0.0976 Hom.: 152

Bravo AF: 0.0870

Asia WGS AF: 0.0290 AC: 103 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.74
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12746613; hg19: chr1-161467042;