ENST00000505018.1:n.60-24377C>G

Variant names:

• chr4-34004663-G-C
• rs7340793
• ENST00000505018.1:n.60-24377C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000505018.1(ENSG00000250954):​n.60-24377C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 150,714 control chromosomes in the GnomAD database, including 2,177 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 0.15 (2177 hom., cov: 31)
• Consequence: ENSG00000250954 ENST00000505018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638
• Publications: 0 publications found

Genes affected

ENSG00000250954 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505018.1. 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
	LOC101928622	NR_125902.1		n.60-24377C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250954	ENST00000505018.1	TSL:1	n.60-24377C>G		intron	N/A
	ENSG00000250954	ENST00000512581.5	TSL:3	n.48+35172C>G		intron	N/A
	ENSG00000250954	ENST00000664054.1		n.80+35172C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22212 AN: 150608 Hom.: 2173 Cov.: 31

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0757

Gnomad MID AF: 0.126

Gnomad NFE AF: 0.0790

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.147 AC: 22222 AN: 150714 Hom.: 2177 Cov.: 31 AF XY: 0.150 AC XY: 11010 AN XY: 73626

African (AFR) AF: 0.258 AC: 10640 AN: 41184

American (AMR) AF: 0.166 AC: 2507 AN: 15090

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 437 AN: 3452

East Asian (EAS) AF: 0.306 AC: 1574 AN: 5138

South Asian (SAS) AF: 0.124 AC: 597 AN: 4804

European-Finnish (FIN) AF: 0.0757 AC: 789 AN: 10416

Middle Eastern (MID) AF: 0.122 AC: 35 AN: 286

European-Non Finnish (NFE) AF: 0.0790 AC: 5321 AN: 67346

Other (OTH) AF: 0.145 AC: 303 AN: 2086

Alfa AF: 0.117 Hom.: 183

Bravo AF: 0.160

Asia WGS AF: 0.233 AC: 808 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.43
DANN	Benign	0.32
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs7340793; hg19: chr4-34006285;