rs55678912

Positions:

• chr2-16051423-C-T

Variant summary

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

The NR_126559.1(GACAT3):​n.251+746C>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 0.0497 in 152,190 control chromosomes in the GnomAD database, including 328 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 0.050 (328 hom., cov: 32)
• Consequence: GACAT3 NR_126559.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220

Genes affected

(HGNC:):

GACAT3 (HGNC:50847): (gastric cancer associated transcript 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GACAT3	NR_126559.1	n.251+746C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000422415.2	n.152+11058G>A		intron_variant, non_coding_transcript_variant		5
GACAT3	ENST00000652394.1	n.353+17118C>T		intron_variant, non_coding_transcript_variant
GACAT3	ENST00000426539.1	n.251+746C>T		intron_variant, non_coding_transcript_variant		3
GACAT3	ENST00000652731.1	n.293+19312C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0496 AC: 7548 AN: 152072 Hom.: 327 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0541

Gnomad ASJ AF: 0.0672

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.00755

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0199

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0497 AC: 7564 AN: 152190 Hom.: 328 Cov.: 32 AF XY: 0.0480 AC XY: 3569 AN XY: 74420

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0541

Gnomad4 ASJ AF: 0.0672

Gnomad4 EAS AF: 0.0186

Gnomad4 SAS AF: 0.0128

Gnomad4 FIN AF: 0.00755

Gnomad4 NFE AF: 0.0199

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0366 Hom.: 33

Bravo AF: 0.0578

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	12
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55678912; hg19: chr2-16191545;