rs9296400

chr6-12508187-T-Achr6-12508187-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.0682

Gnomad4 ASJ AF: 0.0400

Gnomad4 EAS AF: 0.0501

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0207

Gnomad4 NFE AF: 0.0549

Gnomad4 OTH AF: 0.0638

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.90
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9296400; hg19: chr6-12508419;