5-1315228-G-A

Variant names:

• chr5-1315228-G-A
• rs4975615
• ENST00000813113.1:n.1134C>T

Variant summary

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

The ENST00000813113.1(ENSG00000305812):​n.1134C>T 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 0.599 in 152,008 control chromosomes in the GnomAD database, including 27,805 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 0.60 (27805 hom., cov: 32)
• Consequence: ENSG00000305812 ENST00000813113.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 16 publications found

Genes affected

ENSG00000305812 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813113.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305812	ENST00000813113.1		n.1134C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90948 AN: 151890 Hom.: 27790 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.599 AC: 91010 AN: 152008 Hom.: 27805 Cov.: 32 AF XY: 0.605 AC XY: 44935 AN XY: 74272

African (AFR) AF: 0.509 AC: 21123 AN: 41466

American (AMR) AF: 0.704 AC: 10754 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2060 AN: 3468

East Asian (EAS) AF: 0.817 AC: 4225 AN: 5172

South Asian (SAS) AF: 0.811 AC: 3897 AN: 4808

European-Finnish (FIN) AF: 0.556 AC: 5857 AN: 10538

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41131 AN: 67960

Other (OTH) AF: 0.620 AC: 1306 AN: 2108

Alfa AF: 0.606 Hom.: 13862

Bravo AF: 0.603

Asia WGS AF: 0.779 AC: 2708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.51
DANN	Benign	0.45
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs4975615; hg19: chr5-1315343;