rs2173063

Variant names:

• chr15-92588402-G-A
• rs2173063
• ENST00000555864.2:n.216+7181G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-92588402-G-A
• chr15-92588402-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000555864.2(ENSG00000258676):​n.216+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 ENST00000555864.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

Genes affected

ENSG00000258676 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258676	ENST00000555864.2	n.216+7181G>A		intron_variant	Intron 2 of 2	3

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

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.0351

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.0562

Gnomad4 SAS AF: 0.0239

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0629

Gnomad4 OTH AF: 0.0602

Alfa AF: 0.0586 Hom.: 501

Bravo AF: 0.0862

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2173063; hg19: chr15-93131632;