rs1886449

Variant names:

• chr13-73357977-C-T
• rs1886449

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 0.172 in 152,120 control chromosomes in the GnomAD database, including 2,321 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 0.17 (2321 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

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 (EAS) allele frequency at 95% confidence interval = 0.306 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: 0.172 AC: 26084 AN: 152002 Hom.: 2317 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.172 AC: 26099 AN: 152120 Hom.: 2321 Cov.: 32 AF XY: 0.173 AC XY: 12893 AN XY: 74360

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.163

Alfa AF: 0.158 Hom.: 1936

Bravo AF: 0.172

Asia WGS AF: 0.196 AC: 680 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	1.6
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: rs1886449; hg19: chr13-73932114; COSMIC: COSV52393699;