rs9385717

Variant names:

• chr6-135137285-A-G
• rs9385717

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.237 in 152,094 control chromosomes in the GnomAD database, including 4,466 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 (4466 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.73
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 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: 0.237 AC: 35994 AN: 151976 Hom.: 4446 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.237 AC: 36062 AN: 152094 Hom.: 4466 Cov.: 32 AF XY: 0.245 AC XY: 18231 AN XY: 74340

African (AFR) AF: 0.210 AC: 8712 AN: 41488

American (AMR) AF: 0.263 AC: 4017 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 632 AN: 3470

East Asian (EAS) AF: 0.351 AC: 1811 AN: 5162

South Asian (SAS) AF: 0.417 AC: 2008 AN: 4816

European-Finnish (FIN) AF: 0.277 AC: 2932 AN: 10572

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15078 AN: 67980

Other (OTH) AF: 0.270 AC: 570 AN: 2110

Alfa AF: 0.241 Hom.: 2603

Bravo AF: 0.234

Asia WGS AF: 0.422 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	16
DANN	Benign	0.81
PhyloP100		3.7

Splicing

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

Other links and lift over

dbSNP: rs9385717; hg19: chr6-135458423;