rs13199787

Variant names:

• chr6-32737499-C-T
• rs13199787

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;