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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554318.2. 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
	ENSG00000257060	ENST00000554318.2	TSL:3	n.324+46274C>G		intron	N/A
	ENSG00000257060	ENST00000653322.2		n.965-16681C>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4260001;

hg19: chr15-94182862;