rs1348478

Variant names:

• chr5-120098498-G-A
• rs1348478
• ENST00000725215.1:n.100C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-120098498-G-A
• chr5-120098498-G-T

Variant summary

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

The ENST00000725215.1(ENSG00000294678):​n.100C>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 0.307 in 151,536 control chromosomes in the GnomAD database, including 11,690 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 0.31 (11690 hom., cov: 32)
• Consequence: ENSG00000294678 ENST00000725215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 4 publications found

Genes affected

ENSG00000294678 (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 (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294678	ENST00000725215.1	n.100C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46381 AN: 151418 Hom.: 11653 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.307 AC: 46469 AN: 151536 Hom.: 11690 Cov.: 32 AF XY: 0.306 AC XY: 22666 AN XY: 74052

African (AFR) AF: 0.693 AC: 28647 AN: 41360

American (AMR) AF: 0.209 AC: 3166 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 418 AN: 3458

East Asian (EAS) AF: 0.315 AC: 1619 AN: 5134

South Asian (SAS) AF: 0.248 AC: 1193 AN: 4802

European-Finnish (FIN) AF: 0.156 AC: 1635 AN: 10500

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9127 AN: 67794

Other (OTH) AF: 0.266 AC: 560 AN: 2102

Alfa AF: 0.190 Hom.: 14623

Bravo AF: 0.326

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.61
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs1348478; hg19: chr5-119434193;