rs13234380

Positions:

• chr7-36852236-A-G

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 0.278 in 151,806 control chromosomes in the GnomAD database, including 7,467 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 0.28 (7467 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.36852236A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42178 AN: 151688 Hom.: 7469 Cov.: 32

Gnomad AFR AF: 0.0710

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.278 AC: 42165 AN: 151806 Hom.: 7467 Cov.: 32 AF XY: 0.276 AC XY: 20518 AN XY: 74212

Gnomad4 AFR AF: 0.0708

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.283

Alfa AF: 0.358 Hom.: 14666

Bravo AF: 0.256

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.95
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13234380; hg19: chr7-36891841;