rs9301191

Positions:

• chr13-107116756-T-C

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 0.253 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.227

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9301191; hg19: chr13-107769104;