rs9294315

Variant names:

• chr6-84875671-C-G
• rs9294315

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 0.154 in 152,144 control chromosomes in the GnomAD database, including 2,354 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 0.15 (2354 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 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: 0.154 AC: 23454 AN: 152026 Hom.: 2357 Cov.: 32

Gnomad AFR AF: 0.0363

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.154 AC: 23462 AN: 152144 Hom.: 2354 Cov.: 32 AF XY: 0.158 AC XY: 11765 AN XY: 74388

African (AFR) AF: 0.0362 AC: 1504 AN: 41520

American (AMR) AF: 0.221 AC: 3375 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1113 AN: 5180

South Asian (SAS) AF: 0.270 AC: 1302 AN: 4828

European-Finnish (FIN) AF: 0.187 AC: 1978 AN: 10562

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13182 AN: 67978

Other (OTH) AF: 0.145 AC: 306 AN: 2110

Alfa AF: 0.167 Hom.: 327

Bravo AF: 0.151

Asia WGS AF: 0.235 AC: 820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.8
DANN	Benign	0.58
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs9294315; hg19: chr6-85585389;