19-54293995-T-C

Variant names:

• chr19-54293995-T-C
• rs103294
• ENST00000417373.1:n.*54A>G

Variant summary

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

The ENST00000417373.1(ENSG00000240197):​n.*54A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 610,954 control chromosomes in the GnomAD database, including 191,790 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 0.81 (51083 hom., cov: 30)
  • Exomes 𝑓: 0.77 (140707 hom.)
• Consequence: ENSG00000240197 ENST00000417373.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 136 publications found

Genes affected

ENSG00000240197 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417373.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000240197	ENST00000417373.1	TSL:6	n.*54A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123601 AN: 151970 Hom.: 51032 Cov.: 30

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.841

GnomAD4 exome AF: 0.772 AC: 354415 AN: 458866 Hom.: 140707 Cov.: 6 AF XY: 0.780 AC XY: 189621 AN XY: 243102

African (AFR) AF: 0.913 AC: 10654 AN: 11674

American (AMR) AF: 0.700 AC: 14850 AN: 21222

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 9677 AN: 10534

East Asian (EAS) AF: 0.328 AC: 7775 AN: 23680

South Asian (SAS) AF: 0.851 AC: 33342 AN: 39160

European-Finnish (FIN) AF: 0.714 AC: 25566 AN: 35806

Middle Eastern (MID) AF: 0.911 AC: 2922 AN: 3208

European-Non Finnish (NFE) AF: 0.796 AC: 231157 AN: 290536

Other (OTH) AF: 0.802 AC: 18472 AN: 23046

GnomAD4 genome AF: 0.813 AC: 123714 AN: 152088 Hom.: 51083 Cov.: 30 AF XY: 0.808 AC XY: 60057 AN XY: 74370

African (AFR) AF: 0.911 AC: 37777 AN: 41482

American (AMR) AF: 0.781 AC: 11928 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3182 AN: 3470

East Asian (EAS) AF: 0.462 AC: 2388 AN: 5168

South Asian (SAS) AF: 0.838 AC: 4028 AN: 4808

European-Finnish (FIN) AF: 0.706 AC: 7484 AN: 10594

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54080 AN: 67970

Other (OTH) AF: 0.840 AC: 1772 AN: 2110

Alfa AF: 0.802 Hom.: 171067

Bravo AF: 0.814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs103294; hg19: chr19-54797848;