rs1886166

chr13-37616450-A-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 0.294 in 152,008 control chromosomes in the GnomAD database, including 6,992 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 0.29 (6992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 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: 0.294 AC: 44638 AN: 151890 Hom.: 6982 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.294 AC: 44665 AN: 152008 Hom.: 6992 Cov.: 32 AF XY: 0.285 AC XY: 21184 AN XY: 74306

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.312

Alfa AF: 0.324 Hom.: 1039

Bravo AF: 0.294

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.88
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1886166; hg19: chr13-38190587; COSMIC: COSV69347296;