chr5-1315545-G-A

Variant names:

• chr5-1315545-G-A
• rs4975616
• ENST00000813113.1:n.817C>T

Variant summary

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

The ENST00000813113.1(ENSG00000305812):​n.817C>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 0.522 in 152,090 control chromosomes in the GnomAD database, including 22,663 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 0.52 (22663 hom., cov: 32)
• Consequence: ENSG00000305812 ENST00000813113.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 91 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=-0.91).
• 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.817C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79318 AN: 151972 Hom.: 22657 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.522 AC: 79355 AN: 152090 Hom.: 22663 Cov.: 32 AF XY: 0.531 AC XY: 39444 AN XY: 74328

African (AFR) AF: 0.287 AC: 11903 AN: 41498

American (AMR) AF: 0.671 AC: 10257 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1893 AN: 3470

East Asian (EAS) AF: 0.816 AC: 4218 AN: 5166

South Asian (SAS) AF: 0.804 AC: 3870 AN: 4816

European-Finnish (FIN) AF: 0.538 AC: 5688 AN: 10564

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39695 AN: 67972

Other (OTH) AF: 0.561 AC: 1185 AN: 2112

Alfa AF: 0.571 Hom.: 123439

Bravo AF: 0.517

Asia WGS AF: 0.762 AC: 2648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.62
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4975616; hg19: chr5-1315660;