chr18-46762262-A-G

Position:

• chr18-46762262-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663845.1(ST8SIA5-DT):​n.549+1996A>G variant causes a intron, non coding transcript 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 ENST00000663845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST8SIA5-DT	XR_001753435.2	n.1939+1996A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST8SIA5-DT	ENST00000663845.1	n.549+1996A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.559

Alfa AF: 0.468 Hom.: 2162

Bravo AF: 0.575

Asia WGS AF: 0.670 AC: 2330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8085750; hg19: chr18-44342225;