ENST00000466740.2:n.331-3174C>T

Variant names:

• chr17-407766-G-A
• rs4130140
• ENST00000466740.2:n.331-3174C>T

Variant summary

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

The ENST00000466740.2(ENSG00000241525):​n.331-3174C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,072 control chromosomes in the GnomAD database, including 2,510 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 0.18 (2510 hom., cov: 31)
• Consequence: ENSG00000241525 ENST00000466740.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.810
• Publications: 16 publications found

Genes affected

ENSG00000241525 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000466740.2. 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
	LOC105371430	NR_136407.1		n.331-3174C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000241525	ENST00000466740.2	TSL:3	n.331-3174C>T		intron	N/A
	ENSG00000241525	ENST00000599026.1	TSL:5	n.835+1431C>T		intron	N/A
	ENSG00000241525	ENST00000629249.1	TSL:5	n.256-3141C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27108 AN: 151954 Hom.: 2504 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0668

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.178 AC: 27138 AN: 152072 Hom.: 2510 Cov.: 31 AF XY: 0.177 AC XY: 13145 AN XY: 74310

African (AFR) AF: 0.212 AC: 8803 AN: 41476

American (AMR) AF: 0.149 AC: 2275 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3472

East Asian (EAS) AF: 0.0669 AC: 347 AN: 5186

South Asian (SAS) AF: 0.300 AC: 1443 AN: 4812

European-Finnish (FIN) AF: 0.141 AC: 1483 AN: 10526

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11496 AN: 68000

Other (OTH) AF: 0.172 AC: 363 AN: 2112

Alfa AF: 0.176 Hom.: 2489

Bravo AF: 0.177

Asia WGS AF: 0.163 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.86
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs4130140; hg19: chr17-257557;