2-122368903-A-G

Variant names:

• chr2-122368903-A-G
• rs10496584
• ENST00000657880.2:n.755+147984A>G

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.755+147984A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,210 control chromosomes in the GnomAD database, including 2,433 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 0.16 (2433 hom., cov: 32)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587
• Publications: 5 publications found

Genes affected

ENSG00000286481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657880.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286481	ENST00000657880.2		n.755+147984A>G		intron	N/A
	ENSG00000286481	ENST00000819524.1		n.102-24060A>G		intron	N/A
	ENSG00000286481	ENST00000819525.1		n.168+16932A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24124 AN: 152092 Hom.: 2420 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.159 AC: 24173 AN: 152210 Hom.: 2433 Cov.: 32 AF XY: 0.163 AC XY: 12131 AN XY: 74414

African (AFR) AF: 0.160 AC: 6653 AN: 41542

American (AMR) AF: 0.245 AC: 3742 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3472

East Asian (EAS) AF: 0.462 AC: 2389 AN: 5174

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4816

European-Finnish (FIN) AF: 0.127 AC: 1345 AN: 10602

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7633 AN: 68002

Other (OTH) AF: 0.175 AC: 369 AN: 2114

Alfa AF: 0.143 Hom.: 3195

Bravo AF: 0.172

Asia WGS AF: 0.367 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.65
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs10496584; hg19: chr2-123126479;