rs9652236

Variant names:

• chr13-72114636-G-T
• rs9652236

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 0.198 in 152,066 control chromosomes in the GnomAD database, including 3,199 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 0.20 (3199 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 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: 0.198 AC: 30099 AN: 151946 Hom.: 3203 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.198 AC: 30106 AN: 152066 Hom.: 3199 Cov.: 32 AF XY: 0.202 AC XY: 15027 AN XY: 74356

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.193

Alfa AF: 0.176 Hom.: 5110

Bravo AF: 0.208

Asia WGS AF: 0.256 AC: 888 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	0.94
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9652236; hg19: chr13-72688774;