rs2675345

Variant names:

• chr15-48108002-A-G
• rs2675345
• ENST00000730753.1:n.65-613A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-48108002-A-G
• chr15-48108002-A-T

Variant summary

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

The ENST00000730753.1(ENSG00000295542):​n.65-613A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,158 control chromosomes in the GnomAD database, including 15,691 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 0.28 (15691 hom., cov: 32)
• Consequence: ENSG00000295542 ENST00000730753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 24 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 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.65-613A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42646 AN: 152040 Hom.: 15616 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.00424

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.00407

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.281 AC: 42791 AN: 152158 Hom.: 15691 Cov.: 32 AF XY: 0.281 AC XY: 20880 AN XY: 74420

African (AFR) AF: 0.797 AC: 33042 AN: 41458

American (AMR) AF: 0.267 AC: 4087 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3470

East Asian (EAS) AF: 0.735 AC: 3795 AN: 5164

South Asian (SAS) AF: 0.214 AC: 1032 AN: 4826

European-Finnish (FIN) AF: 0.00424 AC: 45 AN: 10620

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.00407 AC: 277 AN: 68006

Other (OTH) AF: 0.224 AC: 473 AN: 2116

Alfa AF: 0.383 Hom.: 8606

Bravo AF: 0.328

Asia WGS AF: 0.567 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.49
DANN	Benign	0.38
PhyloP100		-1.1

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: rs2675345;

hg19: chr15-48400199;