4-57629942-C-T

Variant names:

• chr4-57629942-C-T
• rs17088464
• ENST00000507808.1:n.56-4630G>A

Variant summary

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

The ENST00000507808.1(ENSG00000250333):​n.56-4630G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0479 in 152,146 control chromosomes in the GnomAD database, including 455 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 0.048 (455 hom., cov: 33)
• Consequence: ENSG00000250333 ENST00000507808.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.74
• Publications: 1 publications found

Genes affected

ENSG00000250333 (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 = 0.252 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507808.1. 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
	ENSG00000250333	ENST00000507808.1	TSL:2	n.56-4630G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0478 AC: 7269 AN: 152028 Hom.: 449 Cov.: 33

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.0664

Gnomad FIN AF: 0.0425

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00747

Gnomad OTH AF: 0.0527

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

GnomAD4 genome AF: 0.0479 AC: 7290 AN: 152146 Hom.: 455 Cov.: 33 AF XY: 0.0533 AC XY: 3963 AN XY: 74376

African (AFR) AF: 0.0566 AC: 2350 AN: 41516

American (AMR) AF: 0.137 AC: 2091 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3470

East Asian (EAS) AF: 0.263 AC: 1361 AN: 5166

South Asian (SAS) AF: 0.0660 AC: 318 AN: 4818

European-Finnish (FIN) AF: 0.0425 AC: 450 AN: 10590

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00747 AC: 508 AN: 67996

Other (OTH) AF: 0.0526 AC: 111 AN: 2110

Alfa AF: 0.0261 Hom.: 108

Bravo AF: 0.0563

Asia WGS AF: 0.136 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.70
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs17088464; hg19: chr4-58496108;