chr16-56165393-C-G

Variant names:

• chr16-56165393-C-G
• rs1975634
• ENST00000501259.5:n.1691+22210G>C

Variant summary

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

The ENST00000501259.5(GNAO1-DT):​n.1691+22210G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,978 control chromosomes in the GnomAD database, including 13,535 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 0.42 (13535 hom., cov: 31)
• Consequence: GNAO1-DT ENST00000501259.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000501259.5. 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
	GNAO1-DT	NR_027078.2		n.1691+22210G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNAO1-DT	ENST00000501259.5	TSL:1	n.1691+22210G>C		intron	N/A
	GNAO1-DT	ENST00000565155.3	TSL:2	n.199-13624G>C		intron	N/A
	GNAO1-DT	ENST00000661960.2		n.101-3287G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63629 AN: 151860 Hom.: 13508 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.419 AC: 63701 AN: 151978 Hom.: 13535 Cov.: 31 AF XY: 0.416 AC XY: 30870 AN XY: 74266

African (AFR) AF: 0.370 AC: 15355 AN: 41456

American (AMR) AF: 0.416 AC: 6344 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1784 AN: 3464

East Asian (EAS) AF: 0.319 AC: 1651 AN: 5170

South Asian (SAS) AF: 0.414 AC: 1991 AN: 4812

European-Finnish (FIN) AF: 0.374 AC: 3946 AN: 10556

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31202 AN: 67948

Other (OTH) AF: 0.445 AC: 938 AN: 2110

Alfa AF: 0.433 Hom.: 1777

Bravo AF: 0.420

Asia WGS AF: 0.407 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.8
DANN	Benign	0.59
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1975634; hg19: chr16-56199305;