rs1397148

chr16-56064467-G-A

Variant summary

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

The ENST00000663751.1(GNAO1-DT):n.198-70744C>T 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 0.477 in 151,948 control chromosomes in the GnomAD database, including 17,488 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 0.48 (17488 hom., cov: 32)
• Consequence: GNAO1-DT ENST00000663751.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400

Genes affected

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

LOC105371281 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371281	XR_001752201.2	n.640+776C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNAO1-DT	ENST00000663751.1	n.198-70744C>T		intron_variant, non_coding_transcript_variant
GNAO1-DT	ENST00000668774.1	n.500+11681C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72362 AN: 151830 Hom.: 17461 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.477 AC: 72430 AN: 151948 Hom.: 17488 Cov.: 32 AF XY: 0.474 AC XY: 35170 AN XY: 74250

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.491

Alfa AF: 0.468 Hom.: 2815

Bravo AF: 0.477

Asia WGS AF: 0.443 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1397148; hg19: chr16-56098379;