rs2019091

Variant names:

• chr13-22964921-G-A
• rs2019091
• ENST00000769427.1:n.*80C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000769427.1(ENSG00000300142):​n.*80C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0421 in 151,170 control chromosomes in the GnomAD database, including 80 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 0.042 (80 hom., cov: 40)
• Consequence: ENSG00000300142 ENST00000769427.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 1 publications found

Genes affected

ENSG00000300142 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0421 (6364/151170) while in subpopulation NFE AF = 0.0454 (3062/67468). AF 95% confidence interval is 0.044. There are 80 homozygotes in GnomAd4. There are 3086 alleles in the male GnomAd4 subpopulation. Median coverage is 40. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 80 gene

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
ENSG00000300142	ENST00000769427.1	n.*80C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0420 AC: 6350 AN: 151050 Hom.: 79 Cov.: 40

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0404

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.0449

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0681

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

GnomAD4 genome AF: 0.0421 AC: 6364 AN: 151170 Hom.: 80 Cov.: 40 AF XY: 0.0418 AC XY: 3086 AN XY: 73856

African (AFR) AF: 0.0369 AC: 1527 AN: 41368

American (AMR) AF: 0.0404 AC: 614 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.0818 AC: 282 AN: 3448

East Asian (EAS) AF: 0.00 AC: 0 AN: 5152

South Asian (SAS) AF: 0.0271 AC: 129 AN: 4752

European-Finnish (FIN) AF: 0.0449 AC: 472 AN: 10506

Middle Eastern (MID) AF: 0.138 AC: 40 AN: 290

European-Non Finnish (NFE) AF: 0.0454 AC: 3062 AN: 67468

Other (OTH) AF: 0.0678 AC: 142 AN: 2094

Alfa AF: 0.0526 Hom.: 57

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.22
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs2019091; hg19: chr13-23539060;