rs12746613

chr1-161497252-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0202

Gnomad4 AMR AF: 0.0989

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0853

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0994

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12746613; hg19: chr1-161467042;