rs2444751

Variant names:

• chr15-36485348-C-A
• rs2444751
• ENST00000743889.1:n.377-4866C>A

Your query was ambiguous. Multiple possible variants found:

• chr15-36485348-C-A
• chr15-36485348-C-G
• chr15-36485348-C-T

Variant summary

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

The ENST00000743889.1(ENSG00000296959):​n.377-4866C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,804 control chromosomes in the GnomAD database, including 9,467 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 0.35 (9467 hom., cov: 32)
• Consequence: ENSG00000296959 ENST00000743889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 0 publications found

Genes affected

ENSG00000296959 (HGNC:58973):

LOC105370770 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743889.1. 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
	ENSG00000296959	ENST00000743889.1		n.377-4866C>A		intron	N/A
	ENSG00000296959	ENST00000743890.1		n.239-4866C>A		intron	N/A
	ENSG00000296959	ENST00000743891.1		n.253-4866C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53149 AN: 151686 Hom.: 9454 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.350 AC: 53194 AN: 151804 Hom.: 9467 Cov.: 32 AF XY: 0.352 AC XY: 26104 AN XY: 74166

African (AFR) AF: 0.325 AC: 13458 AN: 41372

American (AMR) AF: 0.470 AC: 7177 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1308 AN: 3468

East Asian (EAS) AF: 0.323 AC: 1663 AN: 5156

South Asian (SAS) AF: 0.252 AC: 1212 AN: 4808

European-Finnish (FIN) AF: 0.382 AC: 4007 AN: 10498

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23169 AN: 67936

Other (OTH) AF: 0.382 AC: 802 AN: 2102

Alfa AF: 0.336 Hom.: 14287

Bravo AF: 0.359

Asia WGS AF: 0.346 AC: 1204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.88
DANN	Benign	0.44
PhyloP100		0.075

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: rs2444751;

hg19: chr15-36777549;