rs13234380

Variant names:

• chr7-36852236-A-G
• rs13234380

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 0.278 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0708 AC: 2929 AN: 41356

American (AMR) AF: 0.241 AC: 3681 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3464

East Asian (EAS) AF: 0.204 AC: 1056 AN: 5164

South Asian (SAS) AF: 0.160 AC: 772 AN: 4814

European-Finnish (FIN) AF: 0.427 AC: 4497 AN: 10536

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27063 AN: 67910

Other (OTH) AF: 0.283 AC: 594 AN: 2100

Alfa AF: 0.348 Hom.: 20187

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
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs13234380; hg19: chr7-36891841;