rs13218732

chr6-152944075-A-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 0.0327 in 152,268 control chromosomes in the GnomAD database, including 82 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 0.033 (82 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0777 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: 0.0327 AC: 4979 AN: 152150 Hom.: 82 Cov.: 33

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.0844

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0396

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0327 AC: 4985 AN: 152268 Hom.: 82 Cov.: 33 AF XY: 0.0326 AC XY: 2425 AN XY: 74456

Gnomad4 AFR AF: 0.0232

Gnomad4 AMR AF: 0.0346

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.0845

Gnomad4 FIN AF: 0.0121

Gnomad4 NFE AF: 0.0397

Gnomad4 OTH AF: 0.0483

Alfa AF: 0.0374 Hom.: 13

Bravo AF: 0.0322

Asia WGS AF: 0.0560 AC: 195 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.072
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: rs13218732; hg19: chr6-153265210;