5-105123252-C-T

Position:

• chr5-105123252-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 0.76 in 151,258 control chromosomes in the GnomAD database, including 48,443 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 0.76 (48443 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.105123252C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000251574	ENST00000503650.1	n.211-236277G>A		intron_variant		3
ENSG00000253584	ENST00000522464.1	n.69-114341G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.760 AC: 114847 AN: 151140 Hom.: 48433 Cov.: 29

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.760 AC: 114890 AN: 151258 Hom.: 48443 Cov.: 29 AF XY: 0.766 AC XY: 56638 AN XY: 73956

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.920

Gnomad4 OTH AF: 0.818

Alfa AF: 0.905 Hom.: 134433

Bravo AF: 0.738

Asia WGS AF: 0.878 AC: 3031 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.46
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs294152; hg19: chr5-104458953;