ENST00000422415.2:n.152+11058G>A

Variant names:

• chr2-16051423-C-T
• rs55678912
• ENST00000422415.2:n.152+11058G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422415.2(ENSG00000226764):​n.152+11058G>A variant causes a intron 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: ENSG00000226764 ENST00000422415.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 3 publications found

Genes affected

ENSG00000226764 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GACAT3	NR_126559.1	n.251+746C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226764	ENST00000422415.2	n.152+11058G>A		intron_variant	Intron 2 of 2	5
GACAT3	ENST00000426539.1	n.251+746C>T		intron_variant	Intron 1 of 3	3
GACAT3	ENST00000652394.1	n.353+17118C>T		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.115 AC: 4789 AN: 41498

American (AMR) AF: 0.0541 AC: 827 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0672 AC: 233 AN: 3468

East Asian (EAS) AF: 0.0186 AC: 96 AN: 5174

South Asian (SAS) AF: 0.0128 AC: 62 AN: 4830

European-Finnish (FIN) AF: 0.00755 AC: 80 AN: 10602

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0199 AC: 1352 AN: 68008

Other (OTH) AF: 0.0464 AC: 98 AN: 2112

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
PhyloP100		-0.022
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs55678912; hg19: chr2-16191545;