12-4715704-A-G

Position:

• chr12-4715704-A-G

Variant summary

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

The NR_110112.1(GAU1):​n.238+4161T>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 0.47 in 152,016 control chromosomes in the GnomAD database, including 17,076 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 (17076 hom., cov: 32)
• Consequence: GAU1 NR_110112.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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=-0.98).
• 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	Protein	UniProt
GAU1	NR_110112.1	n.238+4161T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAU1	ENST00000527518.1	n.238+4161T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71413 AN: 151896 Hom.: 17072 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.470 AC: 71455 AN: 152016 Hom.: 17076 Cov.: 32 AF XY: 0.466 AC XY: 34585 AN XY: 74282

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.437

Alfa AF: 0.482 Hom.: 2189

Bravo AF: 0.474

Asia WGS AF: 0.310 AC: 1083 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.094
DANN	Benign	0.47

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: rs4766282; hg19: chr12-4824870;