18-58416822-T-C

Variant names:

• chr18-58416822-T-C
• rs4503880
• ENST00000585470.1:n.58T>C

Variant summary

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

The ENST00000585470.1(ENSG00000267675):​n.58T>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 0.81 in 152,100 control chromosomes in the GnomAD database, including 50,006 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 0.81 (50006 hom., cov: 34)
  • Exomes 𝑓: 0.77 (34 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000267675 ENST00000585470.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 15 publications found

Genes affected

ENSG00000267675 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585470.1. 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
	ENSG00000267675	ENST00000585470.1	TSL:5	n.58T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000300063	ENST00000768485.1		n.157+2310A>G		intron	N/A
	ENSG00000300063	ENST00000768488.1		n.297+2310A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123112 AN: 151980 Hom.: 49955 Cov.: 34

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.797

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.767 AC: 89 AN: 116 Hom.: 34 Cov.: 0 AF XY: 0.756 AC XY: 65 AN XY: 86

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AF: 0.750 AC: 3 AN: 4

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.833 AC: 5 AN: 6

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.761 AC: 70 AN: 92

Other (OTH) AF: 0.833 AC: 5 AN: 6

GnomAD4 genome AF: 0.810 AC: 123223 AN: 152100 Hom.: 50006 Cov.: 34 AF XY: 0.807 AC XY: 60051 AN XY: 74374

African (AFR) AF: 0.837 AC: 34698 AN: 41470

American (AMR) AF: 0.822 AC: 12571 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2638 AN: 3470

East Asian (EAS) AF: 0.856 AC: 4430 AN: 5178

South Asian (SAS) AF: 0.801 AC: 3862 AN: 4822

European-Finnish (FIN) AF: 0.768 AC: 8118 AN: 10566

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.798 AC: 54257 AN: 67988

Other (OTH) AF: 0.794 AC: 1680 AN: 2116

Alfa AF: 0.821 Hom.: 20263

Bravo AF: 0.814

Asia WGS AF: 0.826 AC: 2871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.45
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4503880; hg19: chr18-56084054;