rs9686327

Variant names:

• chr5-15018428-G-A
• rs9686327

Your query was ambiguous. Multiple possible variants found:

• chr5-15018428-G-A
• chr5-15018428-G-T

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 0.242 in 150,086 control chromosomes in the GnomAD database, including 5,128 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 (5128 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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: 0.242 AC: 36254 AN: 149972 Hom.: 5102 Cov.: 30

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.242 AC: 36332 AN: 150086 Hom.: 5128 Cov.: 30 AF XY: 0.240 AC XY: 17536 AN XY: 73124

African (AFR) AF: 0.391 AC: 15905 AN: 40700

American (AMR) AF: 0.181 AC: 2729 AN: 15066

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 836 AN: 3458

East Asian (EAS) AF: 0.219 AC: 1121 AN: 5114

South Asian (SAS) AF: 0.170 AC: 808 AN: 4752

European-Finnish (FIN) AF: 0.200 AC: 2018 AN: 10076

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12180 AN: 67640

Other (OTH) AF: 0.256 AC: 533 AN: 2078

Alfa AF: 0.202 Hom.: 1828

Bravo AF: 0.248

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs9686327; hg19: chr5-15018537;