5-178708867-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000285978 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638723.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285978	ENST00000638723.1	TSL:5	n.257-1695G>A		intron	N/A	ENSP00000492050.1	A0A1W2PQE6

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

African (AFR) AF: 0.0906 AC: 3760 AN: 41524

American (AMR) AF: 0.243 AC: 3710 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3472

East Asian (EAS) AF: 0.330 AC: 1708 AN: 5172

South Asian (SAS) AF: 0.394 AC: 1899 AN: 4820

European-Finnish (FIN) AF: 0.386 AC: 4066 AN: 10542

Middle Eastern (MID) AF: 0.262 AC: 76 AN: 290

European-Non Finnish (NFE) AF: 0.281 AC: 19084 AN: 67980

Other (OTH) AF: 0.236 AC: 498 AN: 2114

Alfa AF: 0.179 Hom.: 542

Bravo AF: 0.214

Asia WGS AF: 0.363 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.62
PhyloP100		-0.39

Splicing

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

Other links and lift over

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