chr19-50851341-A-T

Variant names:

• chr19-50851341-A-T
• rs2659124
• NR_131203.1:n.*198A>T

Variant summary

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

The NR_131203.1(LOC105372441):​n.*198A>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,048 control chromosomes in the GnomAD database, including 53,417 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 0.84 (53417 hom., cov: 30)
• Consequence: LOC105372441 NR_131203.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 15 publications found

Genes affected

LOC105372441 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372441	NR_131203.1	n.*198A>T		downstream_gene_variant
LOC105372441	NR_131205.1	n.*198A>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126909 AN: 151930 Hom.: 53385 Cov.: 30

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.835 AC: 126993 AN: 152048 Hom.: 53417 Cov.: 30 AF XY: 0.831 AC XY: 61788 AN XY: 74326

African (AFR) AF: 0.845 AC: 35046 AN: 41458

American (AMR) AF: 0.798 AC: 12185 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2664 AN: 3470

East Asian (EAS) AF: 0.592 AC: 3041 AN: 5138

South Asian (SAS) AF: 0.610 AC: 2932 AN: 4810

European-Finnish (FIN) AF: 0.920 AC: 9761 AN: 10606

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58637 AN: 67982

Other (OTH) AF: 0.818 AC: 1726 AN: 2110

Alfa AF: 0.859 Hom.: 6993

Bravo AF: 0.829

Asia WGS AF: 0.621 AC: 2161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2659124; hg19: chr19-51354597;