rs4980202

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105378532 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378532	XR_946421.4	n.2633T>G		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.651

Alfa AF: 0.683 Hom.: 46387

Bravo AF: 0.631

Asia WGS AF: 0.785 AC: 2730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4980202; hg19: chr10-125463604;