chr2-122468047-C-A

Variant names:

• chr2-122468047-C-A
• rs17007761
• ENST00000657880.2:n.756-64804C>A

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.756-64804C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 152,192 control chromosomes in the GnomAD database, including 451 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 0.062 (451 hom., cov: 32)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286481	ENST00000657880.2		n.756-64804C>A		intron	N/A
	ENSG00000287871	ENST00000804613.1		n.165-1013G>T		intron	N/A
	ENSG00000304587	ENST00000804814.1		n.324+1270C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0621 AC: 9447 AN: 152072 Hom.: 450 Cov.: 32

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0396

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0521

Gnomad OTH AF: 0.0661

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

GnomAD4 genome AF: 0.0621 AC: 9453 AN: 152192 Hom.: 451 Cov.: 32 AF XY: 0.0654 AC XY: 4865 AN XY: 74412

African (AFR) AF: 0.0349 AC: 1451 AN: 41526

American (AMR) AF: 0.155 AC: 2371 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3472

East Asian (EAS) AF: 0.101 AC: 523 AN: 5168

South Asian (SAS) AF: 0.160 AC: 771 AN: 4820

European-Finnish (FIN) AF: 0.0396 AC: 419 AN: 10594

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0521 AC: 3541 AN: 68008

Other (OTH) AF: 0.0687 AC: 145 AN: 2110

Alfa AF: 0.0581 Hom.: 1467

Bravo AF: 0.0693

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.65
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs17007761; hg19: chr2-123225623;