rs2298321

Positions:

• chr8-37598786-G-A

Variant summary

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

The ENST00000519691.1(ENSG00000254290):​n.1073C>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 0.0922 in 268,786 control chromosomes in the GnomAD database, including 1,439 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 0.083 (683 hom., cov: 32)
  • Exomes 𝑓: 0.10 (756 hom.)
• Consequence: ENST00000519691.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01605	NR_170186.1	n.779+275C>T		intron_variant, non_coding_transcript_variant
LINC01605	NR_170187.1	n.779+275C>T		intron_variant, non_coding_transcript_variant
LINC01605	NR_170188.1	n.779+275C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000519691.1	n.1073C>T		non_coding_transcript_exon_variant	1/1
	ENST00000522471.1			upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.0830 AC: 12619 AN: 152108 Hom.: 682 Cov.: 32

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.0845

Gnomad EAS AF: 0.0667

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0809

GnomAD4 exome AF: 0.104 AC: 12167 AN: 116560 Hom.: 756 Cov.: 0 AF XY: 0.110 AC XY: 6915 AN XY: 63026

Gnomad4 AFR exome AF: 0.0177

Gnomad4 AMR exome AF: 0.0615

Gnomad4 ASJ exome AF: 0.0742

Gnomad4 EAS exome AF: 0.0396

Gnomad4 SAS exome AF: 0.152

Gnomad4 FIN exome AF: 0.123

Gnomad4 NFE exome AF: 0.0952

Gnomad4 OTH exome AF: 0.0944

GnomAD4 genome AF: 0.0829 AC: 12613 AN: 152226 Hom.: 683 Cov.: 32 AF XY: 0.0858 AC XY: 6386 AN XY: 74432

Gnomad4 AFR AF: 0.0212

Gnomad4 AMR AF: 0.0767

Gnomad4 ASJ AF: 0.0845

Gnomad4 EAS AF: 0.0670

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0800

Alfa AF: 0.0992 Hom.: 1033

Bravo AF: 0.0735

Asia WGS AF: 0.134 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2298321; hg19: chr8-37456304;