10-57158352-C-G

Position:

• chr10-57158352-C-G

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 0.6 in 151,588 control chromosomes in the GnomAD database, including 29,455 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 0.60 (29455 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57158352C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289158	ENST00000690550.1	n.97-49601G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.601 AC: 90959 AN: 151470 Hom.: 29448 Cov.: 30

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.600 AC: 90993 AN: 151588 Hom.: 29455 Cov.: 30 AF XY: 0.603 AC XY: 44656 AN XY: 74064

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.617

Alfa AF: 0.556 Hom.: 1845

Bravo AF: 0.588

Asia WGS AF: 0.693 AC: 2411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.76
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3107503; hg19: chr10-58918112;