rs1975634

chr16-56165393-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027078.2(GNAO1-DT):n.1691+22210G>C variant causes a intron, non coding transcript 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 NR_027078.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNAO1-DT	NR_027078.2	n.1691+22210G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNAO1-DT	ENST00000501259.5	n.1691+22210G>C		intron_variant, non_coding_transcript_variant		1
GNAO1-DT	ENST00000565155.2	n.166-13624G>C		intron_variant, non_coding_transcript_variant		2
GNAO1-DT	ENST00000661960.1	n.101-3287G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.445

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.8
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1975634; hg19: chr16-56199305;