3-47347457-T-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 33 publications found

Genes affected

ENSG00000280173 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.262 AC: 10885 AN: 41482

American (AMR) AF: 0.447 AC: 6830 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1608 AN: 3466

East Asian (EAS) AF: 0.447 AC: 2311 AN: 5170

South Asian (SAS) AF: 0.453 AC: 2183 AN: 4820

European-Finnish (FIN) AF: 0.376 AC: 3972 AN: 10574

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.402 AC: 27321 AN: 67958

Other (OTH) AF: 0.396 AC: 834 AN: 2104

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs8180040; hg19: chr3-47388947;