rs3760627

Positions:

• chr19-44953923-T-C
• chr19-44953923-T-G

Variant summary

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

The ENST00000591646.1(ENSG00000267114):​n.85A>G 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 0.51 in 151,846 control chromosomes in the GnomAD database, including 20,147 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 0.51 (20147 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000267114 ENST00000591646.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

Genes affected

ENSG00000267114 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44953923T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267114	ENST00000591646.1	n.85A>G		non_coding_transcript_exon_variant	1/3	3

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77290 AN: 151726 Hom.: 20114 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.490

GnomAD3 exomes AF: 0.800 AC: 8 AN: 10 Hom.: 3 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad FIN exome AF: 0.500

Gnomad NFE exome AF: 0.875

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.510 AC: 77371 AN: 151844 Hom.: 20147 Cov.: 31 AF XY: 0.512 AC XY: 37991 AN XY: 74188

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.491

Alfa AF: 0.466 Hom.: 34342

Bravo AF: 0.518

Asia WGS AF: 0.577 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760627; hg19: chr19-45457180;