6-91535782-G-C

Variant names:

• chr6-91535782-G-C
• rs9294506

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 0.238 in 151,772 control chromosomes in the GnomAD database, including 4,929 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 (4929 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.389 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: 0.238 AC: 36121 AN: 151656 Hom.: 4929 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.238 AC: 36144 AN: 151772 Hom.: 4929 Cov.: 31 AF XY: 0.245 AC XY: 18153 AN XY: 74164

African (AFR) AF: 0.139 AC: 5760 AN: 41410

American (AMR) AF: 0.397 AC: 6046 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1703 AN: 5122

South Asian (SAS) AF: 0.325 AC: 1563 AN: 4814

European-Finnish (FIN) AF: 0.302 AC: 3179 AN: 10510

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16022 AN: 67906

Other (OTH) AF: 0.252 AC: 532 AN: 2112

Alfa AF: 0.122 Hom.: 210

Bravo AF: 0.242

Asia WGS AF: 0.308 AC: 1071 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.52
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs9294506; hg19: chr6-92245500;