5-105123252-C-T

Variant names:

• chr5-105123252-C-T
• rs294152
• ENST00000503650.1:n.211-236277G>A

Variant summary

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

The ENST00000503650.1(ENSG00000251574):​n.211-236277G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 4 publications found

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503650.1. 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
	ENSG00000251574	ENST00000503650.1	TSL:3	n.211-236277G>A		intron	N/A
	ENSG00000251574	ENST00000522464.1	TSL:3	n.69-114341G>A		intron	N/A
	ENSG00000251574	ENST00000718095.1		n.211-114341G>A		intron	N/A

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

African (AFR) AF: 0.354 AC: 14561 AN: 41154

American (AMR) AF: 0.879 AC: 13359 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3263 AN: 3472

East Asian (EAS) AF: 0.899 AC: 4604 AN: 5120

South Asian (SAS) AF: 0.930 AC: 4481 AN: 4816

European-Finnish (FIN) AF: 0.906 AC: 9495 AN: 10482

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.920 AC: 62284 AN: 67722

Other (OTH) AF: 0.818 AC: 1717 AN: 2098

Alfa AF: 0.899 Hom.: 165911

Bravo AF: 0.738

Asia WGS AF: 0.878 AC: 3031 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.46
DANN	Benign	0.61
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs294152; hg19: chr5-104458953;