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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767027.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299875	ENST00000767027.1		n.*196G>A		downstream_gene	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs473958;

hg19: chr20-919023;