5-180749497-T-C

Variant names:

• chr5-180749497-T-C
• rs6886113

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 0.263 in 152,088 control chromosomes in the GnomAD database, including 5,658 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 0.26 (5658 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 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: 0.263 AC: 39954 AN: 151970 Hom.: 5645 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.263 AC: 39994 AN: 152088 Hom.: 5658 Cov.: 33 AF XY: 0.268 AC XY: 19905 AN XY: 74340

African (AFR) AF: 0.243 AC: 10089 AN: 41468

American (AMR) AF: 0.343 AC: 5244 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 810 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2733 AN: 5178

South Asian (SAS) AF: 0.377 AC: 1816 AN: 4818

European-Finnish (FIN) AF: 0.262 AC: 2766 AN: 10576

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15790 AN: 67990

Other (OTH) AF: 0.250 AC: 528 AN: 2108

Alfa AF: 0.243 Hom.: 18945

Bravo AF: 0.268

Asia WGS AF: 0.425 AC: 1481 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.80
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs6886113; hg19: chr5-180176497;