rs8180040

Positions:

• chr3-47347457-T-A
• chr3-47347457-T-G

Variant summary

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

The ENST00000624214.1(ENSG00000280173):​n.508T>A 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 0.372 in 152,056 control chromosomes in the GnomAD database, including 10,943 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 0.37 (10943 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000280173 ENST00000624214.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

Genes affected

ENSG00000280173 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000280173	ENST00000624214.1	n.508T>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56587 AN: 151940 Hom.: 10940 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.397

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.372 AC: 56600 AN: 152056 Hom.: 10943 Cov.: 32 AF XY: 0.378 AC XY: 28119 AN XY: 74340

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.396

Alfa AF: 0.382 Hom.: 1432

Bravo AF: 0.372

Asia WGS AF: 0.375 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	9.1
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8180040; hg19: chr3-47388947;