5-178998713-T-C

Variant names:

• chr5-178998713-T-C
• rs7733067
• ENST00000521486.1:n.103A>G

Variant summary

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

The ENST00000521486.1(ENSG00000254158):​n.103A>G 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 0.804 in 1,341,180 control chromosomes in the GnomAD database, including 438,279 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 0.71 (38483 hom., cov: 35)
  • Exomes 𝑓: 0.82 (399796 hom.)
• Consequence: ENSG00000254158 ENST00000521486.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.09
• Publications: 3 publications found

Genes affected

ENSG00000254158 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521486.1. 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
	ENSG00000254158	ENST00000521486.1	TSL:6	n.103A>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107330 AN: 152070 Hom.: 38460 Cov.: 35

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.717

GnomAD4 exome AF: 0.816 AC: 970673 AN: 1188992 Hom.: 399796 Cov.: 20 AF XY: 0.813 AC XY: 488951 AN XY: 601324

African (AFR) AF: 0.646 AC: 16544 AN: 25612

American (AMR) AF: 0.727 AC: 29701 AN: 40860

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 19323 AN: 23606

East Asian (EAS) AF: 0.630 AC: 23060 AN: 36600

South Asian (SAS) AF: 0.767 AC: 59524 AN: 77630

European-Finnish (FIN) AF: 0.741 AC: 37115 AN: 50110

Middle Eastern (MID) AF: 0.822 AC: 4045 AN: 4920

European-Non Finnish (NFE) AF: 0.843 AC: 741563 AN: 879436

Other (OTH) AF: 0.793 AC: 39798 AN: 50218

GnomAD4 genome AF: 0.706 AC: 107393 AN: 152188 Hom.: 38483 Cov.: 35 AF XY: 0.705 AC XY: 52441 AN XY: 74394

African (AFR) AF: 0.572 AC: 23753 AN: 41494

American (AMR) AF: 0.720 AC: 11016 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2742 AN: 3470

East Asian (EAS) AF: 0.578 AC: 2989 AN: 5170

South Asian (SAS) AF: 0.721 AC: 3482 AN: 4828

European-Finnish (FIN) AF: 0.732 AC: 7754 AN: 10594

Middle Eastern (MID) AF: 0.779 AC: 226 AN: 290

European-Non Finnish (NFE) AF: 0.781 AC: 53155 AN: 68018

Other (OTH) AF: 0.713 AC: 1507 AN: 2114

Alfa AF: 0.714 Hom.: 5579

Bravo AF: 0.697

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	-0.63
CADD	Benign	12
DANN	Benign	0.67
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs7733067; hg19: chr5-178425714; COSMIC: COSV51434974;