rs693649

Variant names:

• chr20-49571542-G-A
• rs693649
• ENST00000822537.1:n.380G>A

Variant summary

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

The ENST00000822537.1(ENSG00000306999):​n.380G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,954 control chromosomes in the GnomAD database, including 3,545 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 0.21 (3545 hom., cov: 31)
• Consequence: ENSG00000306999 ENST00000822537.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735
• Publications: 11 publications found

Genes affected

ENSG00000306999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822537.1. 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
	ENSG00000306999	ENST00000822537.1		n.380G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31736 AN: 151836 Hom.: 3540 Cov.: 31

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.209 AC: 31758 AN: 151954 Hom.: 3545 Cov.: 31 AF XY: 0.210 AC XY: 15585 AN XY: 74274

African (AFR) AF: 0.182 AC: 7555 AN: 41430

American (AMR) AF: 0.287 AC: 4374 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 546 AN: 3472

East Asian (EAS) AF: 0.376 AC: 1942 AN: 5162

South Asian (SAS) AF: 0.174 AC: 835 AN: 4794

European-Finnish (FIN) AF: 0.229 AC: 2425 AN: 10570

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13281 AN: 67950

Other (OTH) AF: 0.211 AC: 444 AN: 2108

Alfa AF: 0.200 Hom.: 12551

Bravo AF: 0.213

Asia WGS AF: 0.273 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.31
PhyloP100		-0.73

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: rs693649;

hg19: chr20-48188079;