rs9652236

Variant names:

• chr13-72114636-G-T
• rs9652236

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 0.198 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.198 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

African (AFR) AF: 0.232 AC: 9636 AN: 41500

American (AMR) AF: 0.206 AC: 3147 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 803 AN: 3462

East Asian (EAS) AF: 0.419 AC: 2162 AN: 5154

South Asian (SAS) AF: 0.170 AC: 820 AN: 4814

European-Finnish (FIN) AF: 0.161 AC: 1704 AN: 10602

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11128 AN: 67960

Other (OTH) AF: 0.193 AC: 406 AN: 2108

Alfa AF: 0.179 Hom.: 11499

Bravo AF: 0.208

Asia WGS AF: 0.256 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.94
DANN	Benign	0.44
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9652236; hg19: chr13-72688774;