chr15-48092710-A-G

Variant names:

• chr15-48092710-A-G
• rs2250072
• ENST00000730753.1:n.64+11317A>G

Variant summary

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

The ENST00000730753.1(ENSG00000295542):​n.64+11317A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,098 control chromosomes in the GnomAD database, including 17,227 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 (17227 hom., cov: 32)
• Consequence: ENSG00000295542 ENST00000730753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 17 publications found

Genes affected

ENSG00000295542 (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 = 0.876 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730753.1. 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
	ENSG00000295542	ENST00000730753.1		n.64+11317A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51380 AN: 151980 Hom.: 17164 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.339 AC: 51508 AN: 152098 Hom.: 17227 Cov.: 32 AF XY: 0.338 AC XY: 25108 AN XY: 74378

African (AFR) AF: 0.800 AC: 33170 AN: 41466

American (AMR) AF: 0.355 AC: 5432 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0833 AC: 289 AN: 3468

East Asian (EAS) AF: 0.897 AC: 4636 AN: 5166

South Asian (SAS) AF: 0.283 AC: 1367 AN: 4824

European-Finnish (FIN) AF: 0.0414 AC: 439 AN: 10596

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0803 AC: 5462 AN: 67980

Other (OTH) AF: 0.297 AC: 626 AN: 2110

Alfa AF: 0.180 Hom.: 23102

Bravo AF: 0.389

Asia WGS AF: 0.664 AC: 2307 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.57
DANN	Benign	0.61
PhyloP100		-0.43

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: rs2250072;

hg19: chr15-48384907;