chr6-85269737-C-T

Variant names:

• chr6-85269737-C-T
• rs9362176

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 0.0957 in 152,196 control chromosomes in the GnomAD database, including 1,071 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 0.096 (1071 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 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: 0.0957 AC: 14558 AN: 152078 Hom.: 1070 Cov.: 32

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0957 AC: 14564 AN: 152196 Hom.: 1071 Cov.: 32 AF XY: 0.103 AC XY: 7693 AN XY: 74392

African (AFR) AF: 0.0236 AC: 979 AN: 41544

American (AMR) AF: 0.208 AC: 3189 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3472

East Asian (EAS) AF: 0.298 AC: 1545 AN: 5184

South Asian (SAS) AF: 0.203 AC: 981 AN: 4826

European-Finnish (FIN) AF: 0.130 AC: 1372 AN: 10566

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0834 AC: 5672 AN: 67994

Other (OTH) AF: 0.112 AC: 236 AN: 2106

Alfa AF: 0.0946 Hom.: 1591

Bravo AF: 0.0989

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.60
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs9362176; hg19: chr6-85979455;