ENST00000555864.3:n.224+7181G>A

Variant names:

• chr15-92588402-G-A
• rs2173063
• ENST00000555864.3:n.224+7181G>A

Variant summary

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

The ENST00000555864.3(ENSG00000258676):​n.224+7181G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0913 in 152,066 control chromosomes in the GnomAD database, including 876 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 0.091 (876 hom., cov: 32)
• Consequence: ENSG00000258676 ENST00000555864.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 4 publications found

Genes affected

ENSG00000258676 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555864.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258676	ENST00000555864.3	TSL:3	n.224+7181G>A		intron	N/A
	ENSG00000258676	ENST00000812063.1		n.388+7181G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13835 AN: 151948 Hom.: 863 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.0560

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0629

Gnomad OTH AF: 0.0609

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

GnomAD4 genome AF: 0.0913 AC: 13883 AN: 152066 Hom.: 876 Cov.: 32 AF XY: 0.0921 AC XY: 6851 AN XY: 74352

African (AFR) AF: 0.167 AC: 6934 AN: 41460

American (AMR) AF: 0.0351 AC: 537 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3468

East Asian (EAS) AF: 0.0562 AC: 290 AN: 5162

South Asian (SAS) AF: 0.0239 AC: 115 AN: 4816

European-Finnish (FIN) AF: 0.138 AC: 1459 AN: 10580

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0629 AC: 4274 AN: 67980

Other (OTH) AF: 0.0602 AC: 127 AN: 2108

Alfa AF: 0.0663 Hom.: 1266

Bravo AF: 0.0862

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.53
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs2173063; hg19: chr15-93131632;