rs4260001

Variant names:

• chr15-93639633-C-G
• rs4260001
• ENST00000554318.2:n.324+46274C>G

Your query was ambiguous. Multiple possible variants found:

• chr15-93639633-C-G
• chr15-93639633-C-T

Variant summary

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

The ENST00000554318.2(ENSG00000257060):​n.324+46274C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,884 control chromosomes in the GnomAD database, including 9,080 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 0.34 (9080 hom., cov: 30)
• Consequence: ENSG00000257060 ENST00000554318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 0 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983974	XR_001751681.2	n.1032+46900C>G		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257060	ENST00000554318.2	n.324+46274C>G		intron_variant	Intron 3 of 3	3
ENSG00000257060	ENST00000653322.2	n.965-16681C>G		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50948 AN: 151766 Hom.: 9069 Cov.: 30

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.336 AC: 50989 AN: 151884 Hom.: 9080 Cov.: 30 AF XY: 0.351 AC XY: 26061 AN XY: 74228

African (AFR) AF: 0.349 AC: 14458 AN: 41446

American (AMR) AF: 0.383 AC: 5845 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 912 AN: 3468

East Asian (EAS) AF: 0.584 AC: 2999 AN: 5132

South Asian (SAS) AF: 0.490 AC: 2357 AN: 4810

European-Finnish (FIN) AF: 0.465 AC: 4891 AN: 10522

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18447 AN: 67944

Other (OTH) AF: 0.333 AC: 702 AN: 2108

Alfa AF: 0.171 Hom.: 337

Bravo AF: 0.328

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.45
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4260001; hg19: chr15-94182862;