5-178708867-C-T

Variant names:

• chr5-178708867-C-T
• rs1071883
• ENST00000638723.1:n.257-1695G>A

Variant summary

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

The ENST00000638723.1(ENSG00000285978):​n.257-1695G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,098 control chromosomes in the GnomAD database, including 4,949 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 0.24 (4949 hom., cov: 33)
• Consequence: ENSG00000285978 ENST00000638723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

Genes affected

ENSG00000285978 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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.257-1695G>A		intron_variant	Intron 3 of 7	5		ENSP00000492050.1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35915 AN: 151980 Hom.: 4945 Cov.: 33

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.236 AC: 35931 AN: 152098 Hom.: 4949 Cov.: 33 AF XY: 0.245 AC XY: 18184 AN XY: 74320

Gnomad4 AFR AF: 0.0906

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.236

Alfa AF: 0.182 Hom.: 537

Bravo AF: 0.214

Asia WGS AF: 0.363 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1071883; hg19: chr5-178135868; COSMIC: COSV59982523;