4-57629942-C-T

Position:

• chr4-57629942-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.74

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57629942C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000250333	ENST00000507808.1	n.56-4630G>A		intron_variant		2

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

Gnomad4 AFR AF: 0.0566

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0262

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.0660

Gnomad4 FIN AF: 0.0425

Gnomad4 NFE AF: 0.00747

Gnomad4 OTH AF: 0.0526

Alfa AF: 0.0271 Hom.: 104

Bravo AF: 0.0563

Asia WGS AF: 0.136 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17088464; hg19: chr4-58496108;