rs738089

Variant names:

• chr22-20418308-G-A
• rs738089
• ENST00000781077.1:n.-78G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-20418308-G-A
• chr22-20418308-G-C

Variant summary

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

The ENST00000781077.1(ENSG00000301723):​n.-78G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 148,002 control chromosomes in the GnomAD database, including 34,449 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 0.68 (34449 hom., cov: 25)
• Consequence: ENSG00000301723 ENST00000781077.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 9 publications found

Genes affected

ENSG00000301723 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000781077.1. 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
	ENSG00000301723	ENST00000781077.1		n.-78G>A		upstream_gene	N/A
	ENSG00000301723	ENST00000781078.1		n.-113G>A		upstream_gene	N/A
	ENSG00000301723	ENST00000781079.1		n.-2G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.676 AC: 100036 AN: 147930 Hom.: 34437 Cov.: 25

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.676 AC: 100076 AN: 148002 Hom.: 34449 Cov.: 25 AF XY: 0.674 AC XY: 48482 AN XY: 71942

African (AFR) AF: 0.768 AC: 30734 AN: 40012

American (AMR) AF: 0.574 AC: 8512 AN: 14842

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2332 AN: 3444

East Asian (EAS) AF: 0.369 AC: 1835 AN: 4974

South Asian (SAS) AF: 0.557 AC: 2607 AN: 4684

European-Finnish (FIN) AF: 0.734 AC: 6958 AN: 9484

Middle Eastern (MID) AF: 0.642 AC: 185 AN: 288

European-Non Finnish (NFE) AF: 0.670 AC: 45094 AN: 67336

Other (OTH) AF: 0.661 AC: 1349 AN: 2040

Alfa AF: 0.659 Hom.: 18814

Bravo AF: 0.665

Asia WGS AF: 0.511 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.7
DANN	Benign	0.56
PhyloP100		-0.69

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: rs738089;

hg19: chr22-20772598;