2-234260381-G-C

Variant names:

• chr2-234260381-G-C
• rs12998922
• ENST00000760713.1:n.316-14217C>G

Variant summary

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

The ENST00000760713.1(ENSG00000299137):​n.316-14217C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,244 control chromosomes in the GnomAD database, including 2,929 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 0.18 (2929 hom., cov: 32)
• Consequence: ENSG00000299137 ENST00000760713.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 1 publications found

Genes affected

ENSG00000299137 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000760713.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299137	ENST00000760713.1		n.316-14217C>G		intron	N/A
	ENSG00000299137	ENST00000760714.1		n.341-962C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26731 AN: 152126 Hom.: 2930 Cov.: 32

Gnomad AFR AF: 0.0628

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.176 AC: 26723 AN: 152244 Hom.: 2929 Cov.: 32 AF XY: 0.176 AC XY: 13120 AN XY: 74422

African (AFR) AF: 0.0627 AC: 2605 AN: 41572

American (AMR) AF: 0.257 AC: 3934 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3468

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5182

South Asian (SAS) AF: 0.171 AC: 825 AN: 4820

European-Finnish (FIN) AF: 0.180 AC: 1907 AN: 10602

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16078 AN: 68000

Other (OTH) AF: 0.172 AC: 363 AN: 2114

Alfa AF: 0.199 Hom.: 444

Bravo AF: 0.175

Asia WGS AF: 0.0810 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.49
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12998922;

hg19: chr2-235169025;

COSMIC: COSV69023816;