rs9301191

Variant names:

• chr13-107116756-T-C
• rs9301191

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 0.253 in 152,072 control chromosomes in the GnomAD database, including 5,021 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 0.25 (5021 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 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: 0.253 AC: 38519 AN: 151954 Hom.: 5024 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.253 AC: 38536 AN: 152072 Hom.: 5021 Cov.: 32 AF XY: 0.257 AC XY: 19127 AN XY: 74330

African (AFR) AF: 0.274 AC: 11386 AN: 41486

American (AMR) AF: 0.200 AC: 3062 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3470

East Asian (EAS) AF: 0.401 AC: 2072 AN: 5162

South Asian (SAS) AF: 0.332 AC: 1602 AN: 4822

European-Finnish (FIN) AF: 0.301 AC: 3188 AN: 10584

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15699 AN: 67962

Other (OTH) AF: 0.227 AC: 479 AN: 2106

Alfa AF: 0.246 Hom.: 588

Bravo AF: 0.244

Asia WGS AF: 0.363 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.79
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs9301191; hg19: chr13-107769104;