rs33830

Variant names:

• chr5-171721166-T-A
• rs33830
• XR_001742983.2:n.1634-2239A>T

Variant summary

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

The XR_001742983.2(LOC105377724):​n.1634-2239A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,080 control chromosomes in the GnomAD database, including 7,556 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 0.30 (7556 hom., cov: 32)
• Consequence: LOC105377724 XR_001742983.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 4 publications found

Genes affected

LOC105377724 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 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: 0.297 AC: 45084 AN: 151960 Hom.: 7553 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.297 AC: 45097 AN: 152080 Hom.: 7556 Cov.: 32 AF XY: 0.299 AC XY: 22213 AN XY: 74338

African (AFR) AF: 0.151 AC: 6272 AN: 41494

American (AMR) AF: 0.340 AC: 5196 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1487 AN: 3472

East Asian (EAS) AF: 0.400 AC: 2069 AN: 5170

South Asian (SAS) AF: 0.504 AC: 2426 AN: 4812

European-Finnish (FIN) AF: 0.266 AC: 2817 AN: 10572

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23794 AN: 67962

Other (OTH) AF: 0.302 AC: 638 AN: 2112

Alfa AF: 0.318 Hom.: 1039

Bravo AF: 0.291

Asia WGS AF: 0.451 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.73
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs33830; hg19: chr5-171148170; COSMIC: COSV107163904;