rs4980202

Variant names:

• chr10-123704088-A-C
• rs4980202
• XR_946421.4:n.2633T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-123704088-A-C
• chr10-123704088-A-T

Variant summary

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

The XR_946421.4(LOC105378532):​n.2633T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,148 control chromosomes in the GnomAD database, including 31,621 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 0.63 (31621 hom., cov: 33)
• Consequence: LOC105378532 XR_946421.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 7 publications found

Genes affected

LOC105378532 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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: 0.634 AC: 96366 AN: 152030 Hom.: 31596 Cov.: 33

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.634 AC: 96440 AN: 152148 Hom.: 31621 Cov.: 33 AF XY: 0.636 AC XY: 47288 AN XY: 74394

African (AFR) AF: 0.456 AC: 18930 AN: 41478

American (AMR) AF: 0.683 AC: 10449 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2279 AN: 3470

East Asian (EAS) AF: 0.937 AC: 4835 AN: 5162

South Asian (SAS) AF: 0.691 AC: 3335 AN: 4828

European-Finnish (FIN) AF: 0.678 AC: 7198 AN: 10612

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47221 AN: 67990

Other (OTH) AF: 0.651 AC: 1374 AN: 2110

Alfa AF: 0.676 Hom.: 58117

Bravo AF: 0.631

Asia WGS AF: 0.785 AC: 2730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.50
DANN	Benign	0.28
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4980202; hg19: chr10-125463604;