5-181168138-C-T

Variant names:

• chr5-181168138-C-T
• rs1279750

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 0.326 in 151,224 control chromosomes in the GnomAD database, including 12,824 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 0.33 (12824 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 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: 0.326 AC: 49244 AN: 151104 Hom.: 12799 Cov.: 33

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.326 AC: 49322 AN: 151224 Hom.: 12824 Cov.: 33 AF XY: 0.322 AC XY: 23808 AN XY: 73860

African (AFR) AF: 0.708 AC: 29210 AN: 41238

American (AMR) AF: 0.201 AC: 3056 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 838 AN: 3472

East Asian (EAS) AF: 0.219 AC: 1055 AN: 4810

South Asian (SAS) AF: 0.256 AC: 1230 AN: 4814

European-Finnish (FIN) AF: 0.182 AC: 1900 AN: 10424

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.162 AC: 11043 AN: 67992

Other (OTH) AF: 0.291 AC: 609 AN: 2094

Alfa AF: 0.202 Hom.: 7218

Bravo AF: 0.346

Asia WGS AF: 0.284 AC: 972 AN: 3412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.65
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1279750; hg19: chr5-180595138;