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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.260 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

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.260

Alfa AF: 0.265 Hom.: 5312

Bravo AF: 0.258

Asia WGS AF: 0.333 AC: 1160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9507108; hg19: chr13-24077340;