rs1886449

Variant names:

• chr13-73357977-C-T
• rs1886449

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 0.172 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
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.180 AC: 7452 AN: 41500

American (AMR) AF: 0.178 AC: 2719 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3468

East Asian (EAS) AF: 0.319 AC: 1651 AN: 5174

South Asian (SAS) AF: 0.171 AC: 824 AN: 4826

European-Finnish (FIN) AF: 0.200 AC: 2105 AN: 10550

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10271 AN: 67998

Other (OTH) AF: 0.163 AC: 344 AN: 2112

Alfa AF: 0.163 Hom.: 5018

Bravo AF: 0.172

Asia WGS AF: 0.196 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.73
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1886449; hg19: chr13-73932114; COSMIC: COSV52393699;