1-12146595-A-G

Variant names:

• chr1-12146595-A-G
• rs641941

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 0.376 in 152,054 control chromosomes in the GnomAD database, including 11,923 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 0.38 (11923 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 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: 0.376 AC: 57102 AN: 151936 Hom.: 11928 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.376 AC: 57099 AN: 152054 Hom.: 11923 Cov.: 33 AF XY: 0.373 AC XY: 27722 AN XY: 74324

African (AFR) AF: 0.213 AC: 8848 AN: 41476

American (AMR) AF: 0.312 AC: 4777 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1899 AN: 3472

East Asian (EAS) AF: 0.272 AC: 1406 AN: 5174

South Asian (SAS) AF: 0.422 AC: 2030 AN: 4816

European-Finnish (FIN) AF: 0.422 AC: 4464 AN: 10570

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32208 AN: 67940

Other (OTH) AF: 0.420 AC: 886 AN: 2110

Alfa AF: 0.448 Hom.: 21364

Bravo AF: 0.362

Asia WGS AF: 0.324 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.28
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs641941; hg19: chr1-12206652;