19-50840481-G-C

Variant names:

• chr19-50840481-G-C
• rs2659052
• ENST00000598079.1:n.213+9188G>C

Variant summary

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

The ENST00000598079.1(ENSG00000267968):​n.213+9188G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 152,122 control chromosomes in the GnomAD database, including 20,155 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 0.50 (20155 hom., cov: 33)
• Consequence: ENSG00000267968 ENST00000598079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.515
• Publications: 4 publications found

Genes affected

ENSG00000267968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000598079.1. 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
	LOC105372441	NR_131203.1		n.213+9188G>C		intron	N/A
	LOC105372441	NR_131205.1		n.230+9188G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267968	ENST00000598079.1	TSL:3	n.213+9188G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76627 AN: 152004 Hom.: 20150 Cov.: 33

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.504 AC: 76651 AN: 152122 Hom.: 20155 Cov.: 33 AF XY: 0.502 AC XY: 37292 AN XY: 74350

African (AFR) AF: 0.389 AC: 16140 AN: 41510

American (AMR) AF: 0.391 AC: 5984 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1969 AN: 3472

East Asian (EAS) AF: 0.364 AC: 1882 AN: 5172

South Asian (SAS) AF: 0.578 AC: 2792 AN: 4832

European-Finnish (FIN) AF: 0.540 AC: 5706 AN: 10568

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40363 AN: 67958

Other (OTH) AF: 0.526 AC: 1114 AN: 2116

Alfa AF: 0.537 Hom.: 2766

Bravo AF: 0.483

Asia WGS AF: 0.443 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.56
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs2659052; hg19: chr19-51343737;