XR_001751507.3:n.622T>C

Variant names:

• chr15-40963183-T-C
• rs4924524
• XR_001751507.3:n.622T>C

Variant summary

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

The XR_001751507.3(LOC105370789):​n.622T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 151,998 control chromosomes in the GnomAD database, including 30,021 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 0.62 (30021 hom., cov: 32)
• Consequence: LOC105370789 XR_001751507.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 2 publications found

Genes affected

LOC105370789 (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 = 0.784 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795608.1. 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
	ENSG00000303560	ENST00000795608.1		n.375-274T>C		intron	N/A
	ENSG00000303560	ENST00000795609.1		n.*39T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93706 AN: 151880 Hom.: 29981 Cov.: 32

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.617 AC: 93794 AN: 151998 Hom.: 30021 Cov.: 32 AF XY: 0.617 AC XY: 45832 AN XY: 74286

African (AFR) AF: 0.792 AC: 32825 AN: 41466

American (AMR) AF: 0.470 AC: 7172 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1882 AN: 3468

East Asian (EAS) AF: 0.714 AC: 3689 AN: 5170

South Asian (SAS) AF: 0.527 AC: 2532 AN: 4802

European-Finnish (FIN) AF: 0.658 AC: 6957 AN: 10576

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36891 AN: 67930

Other (OTH) AF: 0.579 AC: 1225 AN: 2114

Alfa AF: 0.434 Hom.: 1135

Bravo AF: 0.612

Asia WGS AF: 0.604 AC: 2102 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	1.4
DANN	Benign	0.57
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs4924524; hg19: chr15-41255381;