rs1761455

Variant names:

• chr19-54303579-C-G
• rs1761455
• ENST00000426257.1:n.287-1704G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000426257.1(ENSG00000234436):​n.287-1704G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 151,962 control chromosomes in the GnomAD database, including 41,733 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 0.73 (41733 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000234436 ENST00000426257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 4 publications found

Genes affected

ENSG00000234436 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426257.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234436	ENST00000426257.1	TSL:6	n.287-1704G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110694 AN: 151846 Hom.: 41687 Cov.: 30

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.735

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: 0.729 AC: 110796 AN: 151962 Hom.: 41733 Cov.: 30 AF XY: 0.722 AC XY: 53636 AN XY: 74268

African (AFR) AF: 0.891 AC: 36973 AN: 41486

American (AMR) AF: 0.688 AC: 10498 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2744 AN: 3470

East Asian (EAS) AF: 0.281 AC: 1450 AN: 5156

South Asian (SAS) AF: 0.697 AC: 3353 AN: 4814

European-Finnish (FIN) AF: 0.585 AC: 6158 AN: 10522

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47166 AN: 67940

Other (OTH) AF: 0.732 AC: 1542 AN: 2106

Alfa AF: 0.717 Hom.: 4922

Bravo AF: 0.735

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1761455; hg19: chr19-54814854;