6-9458096-C-T

Variant names:

• chr6-9458096-C-T
• rs761116

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 0.663 in 151,986 control chromosomes in the GnomAD database, including 33,717 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 0.66 (33717 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 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: 0.663 AC: 100691 AN: 151868 Hom.: 33702 Cov.: 33

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.663 AC: 100753 AN: 151986 Hom.: 33717 Cov.: 33 AF XY: 0.661 AC XY: 49068 AN XY: 74284

African (AFR) AF: 0.659 AC: 27306 AN: 41460

American (AMR) AF: 0.659 AC: 10058 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2245 AN: 3470

East Asian (EAS) AF: 0.936 AC: 4824 AN: 5156

South Asian (SAS) AF: 0.764 AC: 3691 AN: 4828

European-Finnish (FIN) AF: 0.515 AC: 5428 AN: 10548

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45102 AN: 67954

Other (OTH) AF: 0.670 AC: 1416 AN: 2112

Alfa AF: 0.655 Hom.: 47578

Bravo AF: 0.671

Asia WGS AF: 0.814 AC: 2828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.79
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs761116; hg19: chr6-9458329;