rs1071882

chr5-178709039-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 0.25 in 152,120 control chromosomes in the GnomAD database, including 5,214 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 0.25 (5214 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 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: 0.250 AC: 37988 AN: 152002 Hom.: 5209 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.250 AC: 38019 AN: 152120 Hom.: 5214 Cov.: 33 AF XY: 0.258 AC XY: 19196 AN XY: 74344

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.247

Alfa AF: 0.281 Hom.: 3523

Bravo AF: 0.230

Asia WGS AF: 0.372 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.2
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1071882; hg19: chr5-178136040; COSMIC: COSV59982538;