18-46762262-A-G

Variant names:

• chr18-46762262-A-G
• rs8085750
• ENST00000624895.1:n.2539A>G

Variant summary

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

The ENST00000624895.1(ST8SIA5-DT):​n.2539A>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 0.566 in 151,996 control chromosomes in the GnomAD database, including 24,958 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 0.57 (24958 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ST8SIA5-DT ENST00000624895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 8 publications found

Genes affected

ST8SIA5-DT (HGNC:55267): (ST8SIA5 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624895.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA5-DT	ENST00000624895.1	TSL:6	n.2539A>G		non_coding_transcript_exon	Exon 1 of 1
	ST8SIA5-DT	ENST00000656102.1		n.551+1996A>G		intron	N/A
	ST8SIA5-DT	ENST00000662459.1		n.549+1996A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85944 AN: 151876 Hom.: 24915 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.552

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.566 AC: 86045 AN: 151994 Hom.: 24958 Cov.: 32 AF XY: 0.569 AC XY: 42260 AN XY: 74298

African (AFR) AF: 0.681 AC: 28223 AN: 41436

American (AMR) AF: 0.583 AC: 8904 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1514 AN: 3466

East Asian (EAS) AF: 0.698 AC: 3600 AN: 5160

South Asian (SAS) AF: 0.523 AC: 2509 AN: 4800

European-Finnish (FIN) AF: 0.553 AC: 5841 AN: 10560

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33931 AN: 67974

Other (OTH) AF: 0.559 AC: 1181 AN: 2114

Alfa AF: 0.478 Hom.: 2343

Bravo AF: 0.575

Asia WGS AF: 0.670 AC: 2330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.33
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs8085750; hg19: chr18-44342225;