rs9635398

Variant names:

• chr15-85802824-G-A
• rs9635398

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 0.355 in 151,968 control chromosomes in the GnomAD database, including 10,432 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 0.36 (10432 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 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: 0.355 AC: 53946 AN: 151850 Hom.: 10419 Cov.: 33

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.355 AC: 53994 AN: 151968 Hom.: 10432 Cov.: 33 AF XY: 0.348 AC XY: 25853 AN XY: 74310

African (AFR) AF: 0.494 AC: 20375 AN: 41284

American (AMR) AF: 0.383 AC: 5857 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3472

East Asian (EAS) AF: 0.123 AC: 638 AN: 5182

South Asian (SAS) AF: 0.224 AC: 1080 AN: 4820

European-Finnish (FIN) AF: 0.257 AC: 2721 AN: 10594

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21394 AN: 68000

Other (OTH) AF: 0.325 AC: 687 AN: 2116

Alfa AF: 0.328 Hom.: 27395

Bravo AF: 0.370

Asia WGS AF: 0.200 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.66
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs9635398; hg19: chr15-86346055;