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. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNAO1-DT	ENST00000663751.1	n.198-11572C>T		intron_variant	Intron 1 of 2
GNAO1-DT	ENST00000668774.1	n.501-13200C>T		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.858

Alfa AF: 0.880 Hom.: 10000

Bravo AF: 0.816

Asia WGS AF: 0.844 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4784621; hg19: chr16-56039207;