22-50565675-C-T

Variant names:

• chr22-50565675-C-T
• rs131766
• XR_001755606.3:n.607+2108C>T

Variant summary

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

The XR_001755606.3(LOC107985568):​n.607+2108C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,924 control chromosomes in the GnomAD database, including 13,453 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 0.40 (13453 hom., cov: 32)
• Consequence: LOC107985568 XR_001755606.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 6 publications found

Genes affected

LOC107985568 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 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: 0.396 AC: 60052 AN: 151804 Hom.: 13450 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.395 AC: 60056 AN: 151924 Hom.: 13453 Cov.: 32 AF XY: 0.398 AC XY: 29574 AN XY: 74226

African (AFR) AF: 0.170 AC: 7043 AN: 41412

American (AMR) AF: 0.439 AC: 6696 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1503 AN: 3468

East Asian (EAS) AF: 0.618 AC: 3202 AN: 5180

South Asian (SAS) AF: 0.362 AC: 1748 AN: 4830

European-Finnish (FIN) AF: 0.519 AC: 5446 AN: 10498

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32921 AN: 67954

Other (OTH) AF: 0.393 AC: 829 AN: 2110

Alfa AF: 0.407 Hom.: 12583

Bravo AF: 0.386

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.62
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs131766; hg19: chr22-51004104;