rs6542736

Positions:

• chr2-107799246-G-A

Variant summary

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

The NR_126370.1(GACAT1):​n.279-11434G>A 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 0.324 in 151,938 control chromosomes in the GnomAD database, including 8,458 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 0.32 (8458 hom., cov: 32)
• Consequence: GACAT1 NR_126370.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247

Genes affected

GACAT1 (HGNC:48336): (gastric cancer associated transcript 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GACAT1	NR_126370.1	n.279-11434G>A		intron_variant, non_coding_transcript_variant
GACAT1	NR_126369.1	n.279-11434G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GACAT1	ENST00000441383.5	n.279-11434G>A		intron_variant, non_coding_transcript_variant		4
GACAT1	ENST00000419650.1	n.246-11434G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49248 AN: 151820 Hom.: 8447 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.324 AC: 49274 AN: 151938 Hom.: 8458 Cov.: 32 AF XY: 0.326 AC XY: 24194 AN XY: 74250

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.344

Alfa AF: 0.366 Hom.: 21213

Bravo AF: 0.318

Asia WGS AF: 0.439 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
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: rs6542736; hg19: chr2-108415702;