15-45981737-C-T

Variant names:

• chr15-45981737-C-T
• rs2507370
• ENST00000773915.1:n.111+32549C>T

Variant summary

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

The ENST00000773915.1(ENSG00000300769):​n.111+32549C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,976 control chromosomes in the GnomAD database, including 8,658 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 0.32 (8658 hom., cov: 32)
• Consequence: ENSG00000300769 ENST00000773915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399
• Publications: 2 publications found

Genes affected

ENSG00000300769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773915.1. 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
	ENSG00000300769	ENST00000773915.1		n.111+32549C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47818 AN: 151858 Hom.: 8630 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0704

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.315 AC: 47895 AN: 151976 Hom.: 8658 Cov.: 32 AF XY: 0.312 AC XY: 23213 AN XY: 74292

African (AFR) AF: 0.498 AC: 20645 AN: 41438

American (AMR) AF: 0.205 AC: 3132 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 980 AN: 3472

East Asian (EAS) AF: 0.0700 AC: 362 AN: 5172

South Asian (SAS) AF: 0.190 AC: 915 AN: 4822

European-Finnish (FIN) AF: 0.289 AC: 3048 AN: 10548

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17929 AN: 67950

Other (OTH) AF: 0.276 AC: 582 AN: 2108

Alfa AF: 0.264 Hom.: 8264

Bravo AF: 0.314

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.64
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs2507370; hg19: chr15-46273935;