rs1681096

Variant names:

• chr12-101210601-G-A
• rs1681096

Your query was ambiguous. Multiple possible variants found:

• chr12-101210601-G-A
• chr12-101210601-G-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 0.489 in 151,964 control chromosomes in the GnomAD database, including 19,001 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 0.49 (19001 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74193 AN: 151848 Hom.: 18985 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.489 AC: 74248 AN: 151964 Hom.: 19001 Cov.: 32 AF XY: 0.490 AC XY: 36408 AN XY: 74252

African (AFR) AF: 0.635 AC: 26308 AN: 41428

American (AMR) AF: 0.413 AC: 6304 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1505 AN: 3472

East Asian (EAS) AF: 0.644 AC: 3327 AN: 5168

South Asian (SAS) AF: 0.384 AC: 1848 AN: 4812

European-Finnish (FIN) AF: 0.508 AC: 5362 AN: 10554

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28110 AN: 67944

Other (OTH) AF: 0.474 AC: 999 AN: 2106

Alfa AF: 0.428 Hom.: 15386

Bravo AF: 0.492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.078
DANN	Benign	0.59
PhyloP100		-1.5
PromoterAI		-0.052	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1681096; hg19: chr12-101604379;