rs1071882

Variant names:

• chr5-178709039-C-T
• rs1071882
• ENST00000638723.1:n.257-1867G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000638723.1(ENSG00000285978):​n.257-1867G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000285978 ENST00000638723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776

Genes affected

ENSG00000285978 (HGNC:):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285978	ENST00000638723.1	n.257-1867G>A		intron_variant	Intron 3 of 7	5		ENSP00000492050.1

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;