rs241257

Variant names:

• chr1-4554762-C-T
• rs241257
• XR_007067009.1:n.545+1259G>A

Variant summary

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

The XR_007067009.1(LOC124904578):​n.545+1259G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,974 control chromosomes in the GnomAD database, including 30,706 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 0.61 (30706 hom., cov: 32)
• Consequence: LOC124904578 XR_007067009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954
• Publications: 4 publications found

Genes affected

LOC124904578 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93108 AN: 151858 Hom.: 30710 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.613 AC: 93116 AN: 151974 Hom.: 30706 Cov.: 32 AF XY: 0.607 AC XY: 45084 AN XY: 74288

African (AFR) AF: 0.451 AC: 18700 AN: 41420

American (AMR) AF: 0.492 AC: 7522 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2468 AN: 3470

East Asian (EAS) AF: 0.152 AC: 782 AN: 5144

South Asian (SAS) AF: 0.555 AC: 2667 AN: 4806

European-Finnish (FIN) AF: 0.750 AC: 7915 AN: 10558

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50731 AN: 67978

Other (OTH) AF: 0.607 AC: 1280 AN: 2108

Alfa AF: 0.687 Hom.: 124819

Bravo AF: 0.588

Asia WGS AF: 0.338 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.029
DANN	Benign	0.71
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs241257; hg19: chr1-4614822;