XR_001739478.1:n.289-21633G>C

Variant names:

• chr2-56627439-G-C
• rs17268959
• XR_001739478.1:n.289-21633G>C

Variant summary

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

The XR_001739478.1(LOC101927213):​n.289-21633G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,828 control chromosomes in the GnomAD database, including 15,458 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 0.43 (15458 hom., cov: 31)
• Consequence: LOC101927213 XR_001739478.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 3 publications found

Genes affected

LOC101927213 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 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: 0.429 AC: 65143 AN: 151710 Hom.: 15454 Cov.: 31

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.429 AC: 65141 AN: 151828 Hom.: 15458 Cov.: 31 AF XY: 0.436 AC XY: 32326 AN XY: 74164

African (AFR) AF: 0.222 AC: 9199 AN: 41414

American (AMR) AF: 0.417 AC: 6345 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1591 AN: 3466

East Asian (EAS) AF: 0.588 AC: 3026 AN: 5148

South Asian (SAS) AF: 0.495 AC: 2387 AN: 4818

European-Finnish (FIN) AF: 0.610 AC: 6419 AN: 10526

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34891 AN: 67912

Other (OTH) AF: 0.454 AC: 957 AN: 2108

Alfa AF: 0.341 Hom.: 999

Bravo AF: 0.405

Asia WGS AF: 0.490 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.54
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs17268959; hg19: chr2-56854574;