19-50850345-A-G

Variant names:

• chr19-50850345-A-G
• rs925013
• ENST00000598079.1:n.214-566A>G

Variant summary

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

The ENST00000598079.1(ENSG00000267968):​n.214-566A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,812 control chromosomes in the GnomAD database, including 3,544 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 0.20 (3544 hom., cov: 31)
• Consequence: ENSG00000267968 ENST00000598079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• Publications: 13 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372441	NR_131203.1	n.214-566A>G		intron_variant	Intron 2 of 2
LOC105372441	NR_131205.1	n.231-566A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267968	ENST00000598079.1	n.214-566A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29928 AN: 151696 Hom.: 3540 Cov.: 31

Gnomad AFR AF: 0.0873

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.197 AC: 29940 AN: 151812 Hom.: 3544 Cov.: 31 AF XY: 0.200 AC XY: 14853 AN XY: 74168

African (AFR) AF: 0.0871 AC: 3611 AN: 41448

American (AMR) AF: 0.301 AC: 4594 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3466

East Asian (EAS) AF: 0.351 AC: 1800 AN: 5124

South Asian (SAS) AF: 0.140 AC: 673 AN: 4796

European-Finnish (FIN) AF: 0.312 AC: 3279 AN: 10514

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14606 AN: 67890

Other (OTH) AF: 0.197 AC: 415 AN: 2108

Alfa AF: 0.206 Hom.: 2633

Bravo AF: 0.193

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.76
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs925013; hg19: chr19-51353601;