6-85191900-C-T

Variant names:

• chr6-85191900-C-T
• rs9294329

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 0.239 in 152,042 control chromosomes in the GnomAD database, including 4,851 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 (4851 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 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: 0.239 AC: 36291 AN: 151924 Hom.: 4853 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.239 AC: 36309 AN: 152042 Hom.: 4851 Cov.: 32 AF XY: 0.241 AC XY: 17924 AN XY: 74306

African (AFR) AF: 0.344 AC: 14235 AN: 41434

American (AMR) AF: 0.298 AC: 4550 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 813 AN: 3472

East Asian (EAS) AF: 0.331 AC: 1712 AN: 5166

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4816

European-Finnish (FIN) AF: 0.188 AC: 1989 AN: 10564

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11137 AN: 67992

Other (OTH) AF: 0.234 AC: 495 AN: 2114

Alfa AF: 0.187 Hom.: 11506

Bravo AF: 0.253

Asia WGS AF: 0.300 AC: 1042 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.2
DANN	Benign	0.84
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs9294329; hg19: chr6-85901618; COSMIC: COSV107167215;