chr5-174791389-C-G

Variant names:

• chr5-174791389-C-G
• rs10476123
• ENST00000502684.1:n.50+40036C>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000502684.1(ENSG00000251670):​n.50+40036C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.00011 (0 hom., cov: 20)
• Consequence: ENSG00000251670 ENST00000502684.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 1 publications found

Genes affected

ENSG00000251670 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502684.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251670	ENST00000502684.1	TSL:5	n.50+40036C>G		intron	N/A
	ENSG00000251670	ENST00000510150.2	TSL:3	n.117-28464C>G		intron	N/A
	ENSG00000251670	ENST00000798403.1		n.179-34733C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000110 AC: 13 AN: 118230 Hom.: 0 Cov.: 20

Gnomad AFR AF: 0.000207

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000979

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000907

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000110 AC: 13 AN: 118304 Hom.: 0 Cov.: 20 AF XY: 0.0000708 AC XY: 4 AN XY: 56528

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000207 AC: 7 AN: 33858

American (AMR) AF: 0.0000978 AC: 1 AN: 10226

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2836

East Asian (EAS) AF: 0.00 AC: 0 AN: 3676

South Asian (SAS) AF: 0.00 AC: 0 AN: 3102

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6966

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 210

European-Non Finnish (NFE) AF: 0.0000908 AC: 5 AN: 55094

Other (OTH) AF: 0.00 AC: 0 AN: 1626

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 6192

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.90
DANN	Benign	0.23
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10476123; hg19: chr5-174218392;