4-58574420-T-C

Position:

• chr4-58574420-T-C

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 0.287 in 151,888 control chromosomes in the GnomAD database, including 6,395 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 0.29 (6395 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.58574420T>C		intergenic_region
LOC107986228	XR_001741512.1	n.394+6740T>C		intron_variant
LOC107986228	XR_002959838.1	n.394+6740T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43577 AN: 151770 Hom.: 6389 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.287 AC: 43604 AN: 151888 Hom.: 6395 Cov.: 32 AF XY: 0.285 AC XY: 21178 AN XY: 74204

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.294

Alfa AF: 0.300 Hom.: 3235

Bravo AF: 0.285

Asia WGS AF: 0.244 AC: 848 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.6
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs704638; hg19: chr4-59440585;