rs318497

Positions:

• chr6-2912043-G-A
• chr6-2912043-G-C
• chr6-2912043-G-T

Variant summary

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

The ENST00000454998.1(ENSG00000232999):​n.71C>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 0.456 in 151,886 control chromosomes in the GnomAD database, including 15,977 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 0.46 (15976 hom., cov: 30)
  • Exomes 𝑓: 0.28 (1 hom.)
• Consequence: ENSG00000232999 ENST00000454998.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

Genes affected

ENSG00000232999 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.2912043G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000232999	ENST00000454998.1	n.71C>T		non_coding_transcript_exon_variant	1/2	6

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69177 AN: 151708 Hom.: 15982 Cov.: 30

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.490

GnomAD4 exome AF: 0.283 AC: 17 AN: 60 Hom.: 1 Cov.: 0 AF XY: 0.235 AC XY: 8 AN XY: 34

Gnomad4 FIN exome AF: 0.273

Gnomad4 NFE exome AF: 0.286

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.456 AC: 69187 AN: 151826 Hom.: 15976 Cov.: 30 AF XY: 0.448 AC XY: 33260 AN XY: 74174

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.487

Alfa AF: 0.476 Hom.: 23995

Bravo AF: 0.471

Asia WGS AF: 0.461 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs318497; hg19: chr6-2912277;