rs12086472

Variant names:

• chr1-150725234-G-A
• rs12086472

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 0.385 in 151,546 control chromosomes in the GnomAD database, including 11,563 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 0.39 (11563 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.532 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: 0.386 AC: 58384 AN: 151430 Hom.: 11553 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.385 AC: 58412 AN: 151546 Hom.: 11563 Cov.: 31 AF XY: 0.390 AC XY: 28854 AN XY: 74000

African (AFR) AF: 0.308 AC: 12720 AN: 41304

American (AMR) AF: 0.436 AC: 6624 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1849 AN: 5162

South Asian (SAS) AF: 0.549 AC: 2643 AN: 4814

European-Finnish (FIN) AF: 0.401 AC: 4165 AN: 10392

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27502 AN: 67894

Other (OTH) AF: 0.396 AC: 835 AN: 2106

Alfa AF: 0.370 Hom.: 4248

Bravo AF: 0.377

Asia WGS AF: 0.392 AC: 1363 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.54
DANN	Benign	0.43
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs12086472; hg19: chr1-150697710;