chr15-48103260-C-T

Variant names:

• chr15-48103260-C-T
• rs78729596
• ENST00000730753.1:n.65-5355C>T

Variant summary

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

The ENST00000730753.1(ENSG00000295542):​n.65-5355C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0132 in 152,286 control chromosomes in the GnomAD database, including 88 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 0.013 (88 hom., cov: 33)
• Consequence: ENSG00000295542 ENST00000730753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0814 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.65-5355C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0130 AC: 1985 AN: 152168 Hom.: 84 Cov.: 33

Gnomad AFR AF: 0.00265

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0749

Gnomad SAS AF: 0.00642

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00115

Gnomad OTH AF: 0.0186

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

GnomAD4 genome AF: 0.0132 AC: 2003 AN: 152286 Hom.: 88 Cov.: 33 AF XY: 0.0149 AC XY: 1111 AN XY: 74464

African (AFR) AF: 0.00265 AC: 110 AN: 41560

American (AMR) AF: 0.0852 AC: 1303 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.0752 AC: 390 AN: 5184

South Asian (SAS) AF: 0.00642 AC: 31 AN: 4826

European-Finnish (FIN) AF: 0.00198 AC: 21 AN: 10618

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00115 AC: 78 AN: 68016

Other (OTH) AF: 0.0189 AC: 40 AN: 2116

Alfa AF: 0.00682 Hom.: 11

Bravo AF: 0.0206

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.6
DANN	Benign	0.49
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs78729596; hg19: chr15-48395457; COSMIC: COSV67907364;