rs9507108

Variant names:

• chr13-23503201-A-C
• rs9507108

Your query was ambiguous. Multiple possible variants found:

• chr13-23503201-A-C
• chr13-23503201-A-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 0.26 in 152,084 control chromosomes in the GnomAD database, including 5,204 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 0.26 (5204 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39556 AN: 151966 Hom.: 5195 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.260 AC: 39587 AN: 152084 Hom.: 5204 Cov.: 32 AF XY: 0.258 AC XY: 19213 AN XY: 74350

African (AFR) AF: 0.220 AC: 9119 AN: 41496

American (AMR) AF: 0.264 AC: 4033 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3472

East Asian (EAS) AF: 0.423 AC: 2174 AN: 5144

South Asian (SAS) AF: 0.266 AC: 1278 AN: 4810

European-Finnish (FIN) AF: 0.269 AC: 2849 AN: 10576

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18848 AN: 67978

Other (OTH) AF: 0.260 AC: 549 AN: 2112

Alfa AF: 0.270 Hom.: 14884

Bravo AF: 0.258

Asia WGS AF: 0.333 AC: 1160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.046
DANN	Benign	0.24
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9507108; hg19: chr13-24077340;