rs17050272

Variant names:

• chr2-120548864-G-A
• rs17050272
• XR_001739681.3:n.2130-2105C>T

Variant summary

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

The XR_001739681.3(LOC105373585):​n.2130-2105C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,102 control chromosomes in the GnomAD database, including 10,407 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 0.34 (10407 hom., cov: 33)
• Consequence: LOC105373585 XR_001739681.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 56 publications found

Genes affected

LOC105373585 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50944 AN: 151984 Hom.: 10396 Cov.: 33

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.335 AC: 50958 AN: 152102 Hom.: 10407 Cov.: 33 AF XY: 0.343 AC XY: 25475 AN XY: 74350

African (AFR) AF: 0.0974 AC: 4044 AN: 41518

American (AMR) AF: 0.407 AC: 6226 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1275 AN: 3470

East Asian (EAS) AF: 0.470 AC: 2425 AN: 5160

South Asian (SAS) AF: 0.300 AC: 1447 AN: 4824

European-Finnish (FIN) AF: 0.552 AC: 5840 AN: 10572

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28524 AN: 67958

Other (OTH) AF: 0.347 AC: 733 AN: 2112

Alfa AF: 0.387 Hom.: 33906

Bravo AF: 0.318

Asia WGS AF: 0.352 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs17050272; hg19: chr2-121306440;