rs2008514

Positions:

• chr16-28814284-G-A

Variant summary

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

The ENST00000469929.1(ENSG00000240634):​n.390C>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 0.35 in 305,744 control chromosomes in the GnomAD database, including 19,823 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 0.35 (9733 hom., cov: 32)
  • Exomes 𝑓: 0.35 (10090 hom.)
• Consequence: ENST00000469929.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.34

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000469929.1	n.390C>T		non_coding_transcript_exon_variant	1/1
	ENST00000507031.2	n.271-1852G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52344 AN: 151644 Hom.: 9702 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.317

GnomAD4 exome AF: 0.355 AC: 54642 AN: 153984 Hom.: 10090 Cov.: 0 AF XY: 0.351 AC XY: 28992 AN XY: 82482

Gnomad4 AFR exome AF: 0.272

Gnomad4 AMR exome AF: 0.474

Gnomad4 ASJ exome AF: 0.284

Gnomad4 EAS exome AF: 0.131

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.393

Gnomad4 NFE exome AF: 0.387

Gnomad4 OTH exome AF: 0.349

GnomAD4 genome AF: 0.346 AC: 52438 AN: 151760 Hom.: 9733 Cov.: 32 AF XY: 0.343 AC XY: 25460 AN XY: 74128

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.321

Alfa AF: 0.379 Hom.: 19452

Bravo AF: 0.344

Asia WGS AF: 0.276 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.62
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2008514; hg19: chr16-28825605;