rs55925192

Variant names:

• chr2-191154393-G-A
• rs55925192
• ENST00000623836.1:n.1678C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-191154393-G-A
• chr2-191154393-G-C

Variant summary

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

The ENST00000623836.1(ENSG00000280083):​n.1678C>T 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 0.556 in 151,872 control chromosomes in the GnomAD database, including 24,935 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 0.56 (24935 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000280083 ENST00000623836.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

Genes affected

ENSG00000280083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 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
ENSG00000280083	ENST00000623836.1	n.1678C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84392 AN: 151754 Hom.: 24921 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.553

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: 0.556 AC: 84451 AN: 151872 Hom.: 24935 Cov.: 31 AF XY: 0.563 AC XY: 41760 AN XY: 74216

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.551

Alfa AF: 0.500 Hom.: 1636

Bravo AF: 0.544

Asia WGS AF: 0.541 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55925192; hg19: chr2-192019119;