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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904578	XR_007067009.1	n.545+1259G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;