rs1279750

chr5-181168138-C-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 0.326 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.291

Alfa AF: 0.195 Hom.: 5016

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1279750; hg19: chr5-180595138;