rs13199787

chr6-32737499-C-T

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 0.388 in 151,786 control chromosomes in the GnomAD database, including 12,943 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 0.39 (12943 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 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: 0.388 AC: 58893 AN: 151670 Hom.: 12931 Cov.: 31

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.388 AC: 58934 AN: 151786 Hom.: 12943 Cov.: 31 AF XY: 0.399 AC XY: 29574 AN XY: 74150

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.394

Alfa AF: 0.405 Hom.: 8296

Bravo AF: 0.374

Asia WGS AF: 0.651 AC: 2253 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	5.2
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13199787; hg19: chr6-32705276;