chr15-73962780-G-T

Variant names:

• chr15-73962780-G-T
• rs10152898
• ENST00000808938.1:n.423+5551G>T

Variant summary

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

The ENST00000808938.1(ENSG00000305125):​n.423+5551G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,086 control chromosomes in the GnomAD database, including 2,147 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 0.16 (2147 hom., cov: 32)
• Consequence: ENSG00000305125 ENST00000808938.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779
• Publications: 7 publications found

Genes affected

ENSG00000305125 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808938.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305125	ENST00000808938.1		n.423+5551G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24908 AN: 151968 Hom.: 2150 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.164 AC: 24916 AN: 152086 Hom.: 2147 Cov.: 32 AF XY: 0.164 AC XY: 12193 AN XY: 74328

African (AFR) AF: 0.156 AC: 6486 AN: 41502

American (AMR) AF: 0.110 AC: 1685 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0764 AC: 265 AN: 3470

East Asian (EAS) AF: 0.130 AC: 674 AN: 5176

South Asian (SAS) AF: 0.131 AC: 629 AN: 4818

European-Finnish (FIN) AF: 0.247 AC: 2606 AN: 10550

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12196 AN: 67980

Other (OTH) AF: 0.130 AC: 273 AN: 2106

Alfa AF: 0.163 Hom.: 9410

Bravo AF: 0.151

Asia WGS AF: 0.144 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.49
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs10152898; hg19: chr15-74255121;