rs9500927

Variant names:

• chr6-32993584-G-A
• rs9500927

Your query was ambiguous. Multiple possible variants found:

• chr6-32993584-G-A
• chr6-32993584-G-C

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 0.192 in 152,164 control chromosomes in the GnomAD database, including 3,243 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 0.19 (3243 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 52 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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: 0.191 AC: 29098 AN: 152046 Hom.: 3225 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0972

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.192 AC: 29151 AN: 152164 Hom.: 3243 Cov.: 32 AF XY: 0.186 AC XY: 13854 AN XY: 74386

African (AFR) AF: 0.314 AC: 13043 AN: 41490

American (AMR) AF: 0.130 AC: 1992 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3472

East Asian (EAS) AF: 0.234 AC: 1209 AN: 5176

South Asian (SAS) AF: 0.0993 AC: 478 AN: 4816

European-Finnish (FIN) AF: 0.0972 AC: 1030 AN: 10592

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10037 AN: 68004

Other (OTH) AF: 0.205 AC: 433 AN: 2110

Alfa AF: 0.164 Hom.: 8599

Bravo AF: 0.203

Asia WGS AF: 0.171 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.64
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs9500927; hg19: chr6-32961361;