rs1797404

Variant names:

• chr12-66186298-G-A
• rs1797404

Your query was ambiguous. Multiple possible variants found:

• chr12-66186298-G-A
• chr12-66186298-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 0.24 in 151,656 control chromosomes in the GnomAD database, including 6,343 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 0.24 (6343 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36384 AN: 151540 Hom.: 6330 Cov.: 30

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.240 AC: 36440 AN: 151656 Hom.: 6343 Cov.: 30 AF XY: 0.241 AC XY: 17870 AN XY: 74130

African (AFR) AF: 0.474 AC: 19538 AN: 41210

American (AMR) AF: 0.149 AC: 2272 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3466

East Asian (EAS) AF: 0.467 AC: 2408 AN: 5160

South Asian (SAS) AF: 0.242 AC: 1164 AN: 4808

European-Finnish (FIN) AF: 0.160 AC: 1687 AN: 10534

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.122 AC: 8301 AN: 67930

Other (OTH) AF: 0.211 AC: 443 AN: 2098

Alfa AF: 0.155 Hom.: 4178

Bravo AF: 0.250

Asia WGS AF: 0.365 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.59
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1797404; hg19: chr12-66580078;