19-51270548-A-G

Variant names:

• chr19-51270548-A-G
• rs1878047
• ENST00000597569.1:n.162-304T>C

Variant summary

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

The ENST00000597569.1(ENSG00000268595):​n.162-304T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,076 control chromosomes in the GnomAD database, including 18,486 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 0.46 (18486 hom., cov: 32)
• Consequence: ENSG00000268595 ENST00000597569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 22 publications found

Genes affected

ENSG00000268595 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000597569.1. 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
	ENSG00000268595	ENST00000597569.1	TSL:4	n.162-304T>C		intron	N/A
	ENSG00000268595	ENST00000716537.1		n.162-304T>C		intron	N/A
	ENSG00000268595	ENST00000716538.1		n.162-304T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70094 AN: 151956 Hom.: 18439 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.433

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.462 AC: 70209 AN: 152076 Hom.: 18486 Cov.: 32 AF XY: 0.458 AC XY: 34058 AN XY: 74322

African (AFR) AF: 0.718 AC: 29784 AN: 41474

American (AMR) AF: 0.509 AC: 7779 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 896 AN: 3466

East Asian (EAS) AF: 0.358 AC: 1850 AN: 5166

South Asian (SAS) AF: 0.229 AC: 1105 AN: 4826

European-Finnish (FIN) AF: 0.357 AC: 3766 AN: 10556

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23792 AN: 67994

Other (OTH) AF: 0.432 AC: 912 AN: 2112

Alfa AF: 0.392 Hom.: 41632

Bravo AF: 0.487

Asia WGS AF: 0.362 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.025
DANN	Benign	0.83
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1878047; hg19: chr19-51773802;