rs234621

Variant names:

• chr20-58915193-C-A
• rs234621
• ENST00000795719.1:n.*5G>T

Variant summary

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

The ENST00000795719.1(ENSG00000303576):​n.*5G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,042 control chromosomes in the GnomAD database, including 7,262 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 0.31 (7262 hom., cov: 32)
• Consequence: ENSG00000303576 ENST00000795719.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992
• Publications: 11 publications found

Genes affected

ENSG00000303576 (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 = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795719.1. 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
	ENSG00000303576	ENST00000795719.1		n.*5G>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47042 AN: 151924 Hom.: 7252 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.310 AC: 47061 AN: 152042 Hom.: 7262 Cov.: 32 AF XY: 0.308 AC XY: 22891 AN XY: 74308

African (AFR) AF: 0.328 AC: 13587 AN: 41462

American (AMR) AF: 0.297 AC: 4533 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1287 AN: 3472

East Asian (EAS) AF: 0.249 AC: 1288 AN: 5176

South Asian (SAS) AF: 0.275 AC: 1329 AN: 4824

European-Finnish (FIN) AF: 0.297 AC: 3143 AN: 10586

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20886 AN: 67962

Other (OTH) AF: 0.304 AC: 641 AN: 2110

Alfa AF: 0.306 Hom.: 30780

Bravo AF: 0.310

Asia WGS AF: 0.253 AC: 878 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	0.097
DANN	Benign	0.68
PhyloP100		-0.99

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: rs234621;

hg19: chr20-57490248;