19-54302487-C-T

Variant names:

• chr19-54302487-C-T
• rs651279
• ENST00000426257.1:n.287-612G>A

Variant summary

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

The ENST00000426257.1(ENSG00000234436):​n.287-612G>A 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 151,974 control chromosomes in the GnomAD database, including 41,710 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 (41700 hom., cov: 30)
  • Exomes 𝑓: 0.88 (10 hom.)
• Consequence: ENSG00000234436 ENST00000426257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 20 publications found

Genes affected

ENSG00000234436 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=1.863).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234436	ENST00000426257.1	TSL:6	n.287-612G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110650 AN: 151830 Hom.: 41658 Cov.: 30

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.735

GnomAD4 exome AF: 0.885 AC: 23 AN: 26 Hom.: 10 Cov.: 0 AF XY: 0.850 AC XY: 17 AN XY: 20

African (AFR) AF: 1.00 AC: 2 AN: 2

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) AF: 0.850 AC: 17 AN: 20

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.729 AC: 110749 AN: 151948 Hom.: 41700 Cov.: 30 AF XY: 0.722 AC XY: 53588 AN XY: 74236

African (AFR) AF: 0.890 AC: 36904 AN: 41458

American (AMR) AF: 0.687 AC: 10484 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2729 AN: 3468

East Asian (EAS) AF: 0.280 AC: 1444 AN: 5152

South Asian (SAS) AF: 0.697 AC: 3349 AN: 4808

European-Finnish (FIN) AF: 0.586 AC: 6165 AN: 10520

Middle Eastern (MID) AF: 0.818 AC: 239 AN: 292

European-Non Finnish (NFE) AF: 0.695 AC: 47217 AN: 67976

Other (OTH) AF: 0.732 AC: 1545 AN: 2110

Alfa AF: 0.702 Hom.: 137988

Bravo AF: 0.735

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.9
PhyloP100		-0.93

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs651279;