chr2-122368903-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373592	XR_001739684.2	n.753-24060A>G		intron_variant	Intron 3 of 6
LOC105373592	XR_007087222.1	n.753-24060A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286481	ENST00000657880.2	n.755+147984A>G		intron_variant	Intron 3 of 8
ENSG00000286481	ENST00000819524.1	n.102-24060A>G		intron_variant	Intron 1 of 2
ENSG00000286481	ENST00000819525.1	n.168+16932A>G		intron_variant	Intron 1 of 2
ENSG00000286481	ENST00000819526.1	n.121+16932A>G		intron_variant	Intron 1 of 3

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 v4.3

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;