rs4784621

Variant names:

• chr16-56005295-G-A
• rs4784621
• ENST00000663751.1:n.198-11572C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-56005295-G-A
• chr16-56005295-G-C

Variant summary

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

The ENST00000663751.1(GNAO1-DT):​n.198-11572C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,052 control chromosomes in the GnomAD database, including 54,977 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 0.84 (54977 hom., cov: 30)
• Consequence: GNAO1-DT ENST00000663751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 3 publications found

Genes affected

GNAO1-DT (HGNC:27543): (GNAO1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663751.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNAO1-DT	ENST00000663751.1		n.198-11572C>T		intron	N/A
	GNAO1-DT	ENST00000668774.1		n.501-13200C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127209 AN: 151934 Hom.: 54956 Cov.: 30

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.837 AC: 127272 AN: 152052 Hom.: 54977 Cov.: 30 AF XY: 0.838 AC XY: 62301 AN XY: 74334

African (AFR) AF: 0.603 AC: 24958 AN: 41400

American (AMR) AF: 0.822 AC: 12560 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3263 AN: 3472

East Asian (EAS) AF: 0.869 AC: 4469 AN: 5144

South Asian (SAS) AF: 0.901 AC: 4337 AN: 4814

European-Finnish (FIN) AF: 0.958 AC: 10173 AN: 10616

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64547 AN: 68006

Other (OTH) AF: 0.858 AC: 1816 AN: 2116

Alfa AF: 0.872 Hom.: 10133

Bravo AF: 0.816

Asia WGS AF: 0.844 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.35
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs4784621; hg19: chr16-56039207;