rs4765780

chr12-4714793-G-Achr12-4714793-G-C

Variant summary

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

The NR_110112.1(GAU1):n.238+5072C>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 0.47 in 151,980 control chromosomes in the GnomAD database, including 17,074 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 0.47 (17074 hom., cov: 31)
• Consequence: GAU1 NR_110112.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

Genes affected

GAU1 (HGNC:53880): (GALNT8 antisense upstream 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAU1	NR_110112.1	n.238+5072C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAU1	ENST00000527518.1	n.238+5072C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71368 AN: 151862 Hom.: 17070 Cov.: 31

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.470 AC: 71410 AN: 151980 Hom.: 17074 Cov.: 31 AF XY: 0.465 AC XY: 34574 AN XY: 74280

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.437

Alfa AF: 0.474 Hom.: 2074

Bravo AF: 0.473

Asia WGS AF: 0.311 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.5
Dann	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4765780; hg19: chr12-4823959;