rs473958

Variant names:

• chr20-938380-G-A
• rs473958
• ENST00000767027.1:n.*196G>A

Variant summary

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

The ENST00000767027.1(ENSG00000299875):​n.*196G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,812 control chromosomes in the GnomAD database, including 11,261 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 0.38 (11261 hom., cov: 31)
• Consequence: ENSG00000299875 ENST00000767027.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 0 publications found

Genes affected

ENSG00000299875 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372492	XR_937185.3	n.*164G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299875	ENST00000767027.1	n.*196G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57486 AN: 151694 Hom.: 11259 Cov.: 31

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.379 AC: 57514 AN: 151812 Hom.: 11261 Cov.: 31 AF XY: 0.374 AC XY: 27719 AN XY: 74202

African (AFR) AF: 0.450 AC: 18604 AN: 41376

American (AMR) AF: 0.290 AC: 4425 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1468 AN: 3468

East Asian (EAS) AF: 0.164 AC: 844 AN: 5160

South Asian (SAS) AF: 0.265 AC: 1272 AN: 4800

European-Finnish (FIN) AF: 0.341 AC: 3595 AN: 10540

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.383 AC: 26022 AN: 67910

Other (OTH) AF: 0.349 AC: 735 AN: 2104

Alfa AF: 0.387 Hom.: 2418

Bravo AF: 0.378

Asia WGS AF: 0.245 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.71
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs473958; hg19: chr20-919023;