rs13199787

Variant names:

• chr6-32737499-C-T
• rs13199787

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 0.388 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
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.207 AC: 8597 AN: 41438

American (AMR) AF: 0.444 AC: 6774 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1470 AN: 3468

East Asian (EAS) AF: 0.752 AC: 3865 AN: 5140

South Asian (SAS) AF: 0.602 AC: 2904 AN: 4820

European-Finnish (FIN) AF: 0.535 AC: 5584 AN: 10434

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28152 AN: 67908

Other (OTH) AF: 0.394 AC: 832 AN: 2112

Alfa AF: 0.406 Hom.: 13921

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
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs13199787; hg19: chr6-32705276;