rs12034888

Variant names:

• chr1-182568661-G-A
• rs12034888

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 0.072 in 152,152 control chromosomes in the GnomAD database, including 468 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 0.072 (468 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 0 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 = 0.14 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: 0.0720 AC: 10952 AN: 152034 Hom.: 470 Cov.: 33

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0751

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0991

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0720 AC: 10948 AN: 152152 Hom.: 468 Cov.: 33 AF XY: 0.0727 AC XY: 5411 AN XY: 74378

African (AFR) AF: 0.0390 AC: 1620 AN: 41524

American (AMR) AF: 0.0749 AC: 1146 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3472

East Asian (EAS) AF: 0.0987 AC: 511 AN: 5176

South Asian (SAS) AF: 0.149 AC: 719 AN: 4818

European-Finnish (FIN) AF: 0.0554 AC: 585 AN: 10566

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0829 AC: 5636 AN: 67984

Other (OTH) AF: 0.0937 AC: 198 AN: 2114

Alfa AF: 0.0685 Hom.: 54

Bravo AF: 0.0708

Asia WGS AF: 0.155 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.2
DANN	Benign	0.64
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs12034888; hg19: chr1-182537796;