ENST00000591646.1:n.113+47T>C

Variant names:

• chr19-44953848-A-G
• rs3760626
• ENST00000591646.1:n.113+47T>C

Variant summary

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

The ENST00000591646.1(ENSG00000267114):​n.113+47T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,830 control chromosomes in the GnomAD database, including 21,321 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 0.52 (21321 hom., cov: 30)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: ENSG00000267114 ENST00000591646.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

ENSG00000267114 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 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
ENSG00000267114	ENST00000591646.1	n.113+47T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79196 AN: 151706 Hom.: 21287 Cov.: 30

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.500

GnomAD3 exomes AF: 0.800 AC: 8 AN: 10 Hom.: 3 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad AFR exome AF: 1.00

Gnomad ASJ exome AF: 0.500

Gnomad FIN exome AF: 1.00

Gnomad NFE exome AF: 0.750

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 NFE exome AF: 0.167

GnomAD4 genome AF: 0.522 AC: 79278 AN: 151824 Hom.: 21321 Cov.: 30 AF XY: 0.525 AC XY: 38906 AN XY: 74176

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.501

Alfa AF: 0.497 Hom.: 2332

Bravo AF: 0.533

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760626; hg19: chr19-45457105;