19-54296519-C-T

Variant names:

• chr19-54296519-C-T
• rs410852
• ENST00000733241.1:n.154-267G>A

Variant summary

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

The ENST00000733241.1(ENSG00000295857):​n.154-267G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 352,474 control chromosomes in the GnomAD database, including 68,477 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 0.55 (25301 hom., cov: 30)
  • Exomes 𝑓: 0.64 (43176 hom.)
• Consequence: ENSG00000295857 ENST00000733241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 18 publications found

Genes affected

ENSG00000295857 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 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
ENSG00000295857	ENST00000733241.1	n.154-267G>A		intron_variant	Intron 2 of 2
ENSG00000295857	ENST00000733242.1	n.186-267G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83025 AN: 151694 Hom.: 25307 Cov.: 30

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.610

GnomAD4 exome AF: 0.644 AC: 129284 AN: 200662 Hom.: 43176 Cov.: 4 AF XY: 0.644 AC XY: 71851 AN XY: 111546

African (AFR) AF: 0.287 AC: 1339 AN: 4660

American (AMR) AF: 0.457 AC: 3964 AN: 8678

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 3539 AN: 4372

East Asian (EAS) AF: 0.244 AC: 1700 AN: 6970

South Asian (SAS) AF: 0.643 AC: 25656 AN: 39930

European-Finnish (FIN) AF: 0.610 AC: 5230 AN: 8578

Middle Eastern (MID) AF: 0.804 AC: 545 AN: 678

European-Non Finnish (NFE) AF: 0.692 AC: 81187 AN: 117380

Other (OTH) AF: 0.650 AC: 6124 AN: 9416

GnomAD4 genome AF: 0.547 AC: 83041 AN: 151812 Hom.: 25301 Cov.: 30 AF XY: 0.543 AC XY: 40287 AN XY: 74182

African (AFR) AF: 0.307 AC: 12694 AN: 41350

American (AMR) AF: 0.498 AC: 7606 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2802 AN: 3470

East Asian (EAS) AF: 0.258 AC: 1334 AN: 5164

South Asian (SAS) AF: 0.627 AC: 3013 AN: 4804

European-Finnish (FIN) AF: 0.597 AC: 6275 AN: 10504

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47113 AN: 67940

Other (OTH) AF: 0.612 AC: 1287 AN: 2104

Alfa AF: 0.642 Hom.: 51788

Bravo AF: 0.522

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs410852; hg19: chr19-54800371;