rs12085006

Variant names:

• chr1-11898666-A-G
• rs12085006

Your query was ambiguous. Multiple possible variants found:

• chr1-11898666-A-G
• chr1-11898666-A-T

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 0.543 in 151,870 control chromosomes in the GnomAD database, including 23,373 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 0.54 (23373 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 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: 0.543 AC: 82335 AN: 151752 Hom.: 23324 Cov.: 31

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.543 AC: 82450 AN: 151870 Hom.: 23373 Cov.: 31 AF XY: 0.548 AC XY: 40650 AN XY: 74210

African (AFR) AF: 0.691 AC: 28601 AN: 41420

American (AMR) AF: 0.441 AC: 6725 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1198 AN: 3470

East Asian (EAS) AF: 0.622 AC: 3191 AN: 5134

South Asian (SAS) AF: 0.655 AC: 3154 AN: 4818

European-Finnish (FIN) AF: 0.603 AC: 6358 AN: 10548

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31656 AN: 67922

Other (OTH) AF: 0.514 AC: 1080 AN: 2102

Alfa AF: 0.500 Hom.: 33680

Bravo AF: 0.531

Asia WGS AF: 0.672 AC: 2338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.25
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs12085006; hg19: chr1-11958723;