rs8180040

Variant names:

• chr3-47347457-T-A
• rs8180040
• ENST00000624214.1:n.508T>A

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000280173	ENST00000624214.1	n.508T>A		non_coding_transcript_exon_variant	Exon 1 of 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;