rs3760627

Variant names:

• chr19-44953923-T-C
• rs3760627
• ENST00000591646.1:n.85A>G

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267114	ENST00000591646.1	n.85A>G		non_coding_transcript_exon_variant	Exon 1 of 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;