rs17049450

Variant names:

• chr2-129427605-A-G
• rs17049450
• XR_007088752.1:n.*80A>G

Variant summary

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

The XR_007088752.1(LOC124906164):​n.*80A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,104 control chromosomes in the GnomAD database, including 22,541 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 0.49 (22541 hom., cov: 33)
• Consequence: LOC124906164 XR_007088752.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 1 publications found

Genes affected

LOC124906164 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75174 AN: 151986 Hom.: 22544 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.494 AC: 75176 AN: 152104 Hom.: 22541 Cov.: 33 AF XY: 0.496 AC XY: 36889 AN XY: 74356

African (AFR) AF: 0.147 AC: 6089 AN: 41532

American (AMR) AF: 0.511 AC: 7812 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2107 AN: 3470

East Asian (EAS) AF: 0.335 AC: 1723 AN: 5150

South Asian (SAS) AF: 0.625 AC: 3009 AN: 4814

European-Finnish (FIN) AF: 0.636 AC: 6719 AN: 10558

Middle Eastern (MID) AF: 0.486 AC: 141 AN: 290

European-Non Finnish (NFE) AF: 0.675 AC: 45880 AN: 67988

Other (OTH) AF: 0.503 AC: 1063 AN: 2114

Alfa AF: 0.571 Hom.: 3406

Bravo AF: 0.468

Asia WGS AF: 0.434 AC: 1512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.69
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs17049450; hg19: chr2-130185178;