rs12031680

Variant names:

• chr1-84069614-C-A
• rs12031680

Your query was ambiguous. Multiple possible variants found:

• chr1-84069614-C-A
• chr1-84069614-C-G
• chr1-84069614-C-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 0.435 in 151,774 control chromosomes in the GnomAD database, including 15,512 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 0.43 (15512 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 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: 0.435 AC: 65960 AN: 151652 Hom.: 15503 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.435 AC: 66002 AN: 151774 Hom.: 15512 Cov.: 32 AF XY: 0.440 AC XY: 32622 AN XY: 74172

African (AFR) AF: 0.576 AC: 23869 AN: 41406

American (AMR) AF: 0.487 AC: 7428 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1558 AN: 3472

East Asian (EAS) AF: 0.604 AC: 3116 AN: 5156

South Asian (SAS) AF: 0.466 AC: 2242 AN: 4814

European-Finnish (FIN) AF: 0.371 AC: 3895 AN: 10504

Middle Eastern (MID) AF: 0.528 AC: 152 AN: 288

European-Non Finnish (NFE) AF: 0.332 AC: 22511 AN: 67848

Other (OTH) AF: 0.419 AC: 884 AN: 2110

Alfa AF: 0.387 Hom.: 2263

Bravo AF: 0.453

Asia WGS AF: 0.485 AC: 1670 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.91
DANN	Benign	0.14
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12031680; hg19: chr1-84535297;