rs9296400

Variant names:

• chr6-12508187-T-A
• rs9296400

Your query was ambiguous. Multiple possible variants found:

• chr6-12508187-T-A
• chr6-12508187-T-C

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 0.0703 in 152,282 control chromosomes in the GnomAD database, including 457 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 0.070 (457 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.108 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: 0.0703 AC: 10698 AN: 152164 Hom.: 452 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0682

Gnomad ASJ AF: 0.0400

Gnomad EAS AF: 0.0508

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0207

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0549

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0703 AC: 10710 AN: 152282 Hom.: 457 Cov.: 33 AF XY: 0.0706 AC XY: 5259 AN XY: 74462

African (AFR) AF: 0.111 AC: 4606 AN: 41562

American (AMR) AF: 0.0682 AC: 1043 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0400 AC: 139 AN: 3472

East Asian (EAS) AF: 0.0501 AC: 260 AN: 5186

South Asian (SAS) AF: 0.115 AC: 556 AN: 4832

European-Finnish (FIN) AF: 0.0207 AC: 220 AN: 10618

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0549 AC: 3731 AN: 68006

Other (OTH) AF: 0.0638 AC: 135 AN: 2116

Alfa AF: 0.0195 Hom.: 9

Bravo AF: 0.0714

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.90
DANN	Benign	0.33
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs9296400; hg19: chr6-12508419;