rs17007761

Variant names:

• chr2-122468047-C-A
• rs17007761
• ENST00000657880.1:n.705-64804C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657880.1(ENSG00000286481):​n.705-64804C>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 ENST00000657880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

ENSG00000286481 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286481	ENST00000657880.1	n.705-64804C>A		intron_variant	Intron 3 of 8

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

Gnomad4 AFR AF: 0.0349

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0396

Gnomad4 NFE AF: 0.0521

Gnomad4 OTH AF: 0.0687

Alfa AF: 0.0594 Hom.: 750

Bravo AF: 0.0693

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17007761; hg19: chr2-123225623;