rs2388883

Variant names:

• chr15-94777905-A-G
• rs2388883
• ENST00000722729.1:n.359-11888T>C

Variant summary

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

The ENST00000722729.1(ENSG00000294319):​n.359-11888T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,080 control chromosomes in the GnomAD database, including 8,854 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 0.31 (8854 hom., cov: 32)
• Consequence: ENSG00000294319 ENST00000722729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 3 publications found

Genes affected

ENSG00000294319 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722729.1. 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
	ENSG00000294319	ENST00000722729.1		n.359-11888T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46533 AN: 151962 Hom.: 8825 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.306 AC: 46611 AN: 152080 Hom.: 8854 Cov.: 32 AF XY: 0.307 AC XY: 22820 AN XY: 74366

African (AFR) AF: 0.537 AC: 22246 AN: 41458

American (AMR) AF: 0.261 AC: 3982 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 758 AN: 3472

East Asian (EAS) AF: 0.199 AC: 1027 AN: 5168

South Asian (SAS) AF: 0.128 AC: 615 AN: 4822

European-Finnish (FIN) AF: 0.330 AC: 3489 AN: 10584

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13616 AN: 67990

Other (OTH) AF: 0.304 AC: 639 AN: 2104

Alfa AF: 0.228 Hom.: 3558

Bravo AF: 0.313

Asia WGS AF: 0.228 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.62
PhyloP100		0.058

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: rs2388883;

hg19: chr15-95321134;