rs2298320

chr8-37598920-A-Gchr8-37598920-A-T

Variant summary

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

The ENST00000519691.1(ENSG00000254290):n.939T>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 0.462 in 166,452 control chromosomes in the GnomAD database, including 18,148 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 0.47 (16817 hom., cov: 32)
  • Exomes 𝑓: 0.41 (1331 hom.)
• Consequence: ENST00000519691.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01605	NR_170186.1	n.779+141T>C		intron_variant, non_coding_transcript_variant
LINC01605	NR_170187.1	n.779+141T>C		intron_variant, non_coding_transcript_variant
LINC01605	NR_170188.1	n.779+141T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000519691.1	n.939T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70868 AN: 151928 Hom.: 16783 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.462

GnomAD4 exome AF: 0.412 AC: 5940 AN: 14406 Hom.: 1331 Cov.: 0 AF XY: 0.417 AC XY: 3048 AN XY: 7308

Gnomad4 AFR exome AF: 0.315

Gnomad4 AMR exome AF: 0.397

Gnomad4 ASJ exome AF: 0.368

Gnomad4 EAS exome AF: 0.431

Gnomad4 SAS exome AF: 0.367

Gnomad4 FIN exome AF: 0.488

Gnomad4 NFE exome AF: 0.421

Gnomad4 OTH exome AF: 0.391

GnomAD4 genome AF: 0.467 AC: 70962 AN: 152046 Hom.: 16817 Cov.: 32 AF XY: 0.473 AC XY: 35144 AN XY: 74304

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.463

Alfa AF: 0.480 Hom.: 2922

Bravo AF: 0.457

Asia WGS AF: 0.469 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.83
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2298320; hg19: chr8-37456438;