chr10-130193981-A-G

Variant names:

• chr10-130193981-A-G
• rs4751178
• XM_047426136.1:c.*2756A>G

Variant summary

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

The XM_047426136.1(LOC124902561):​c.*2756A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 151,900 control chromosomes in the GnomAD database, including 40,861 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 0.73 (40861 hom., cov: 30)
• Consequence: LOC124902561 XM_047426136.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 8 publications found

Genes affected

LOC124902561 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 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: 0.733 AC: 111201 AN: 151782 Hom.: 40826 Cov.: 30

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.733 AC: 111291 AN: 151900 Hom.: 40861 Cov.: 30 AF XY: 0.734 AC XY: 54467 AN XY: 74250

African (AFR) AF: 0.802 AC: 33214 AN: 41416

American (AMR) AF: 0.704 AC: 10752 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2598 AN: 3468

East Asian (EAS) AF: 0.678 AC: 3486 AN: 5142

South Asian (SAS) AF: 0.714 AC: 3435 AN: 4810

European-Finnish (FIN) AF: 0.706 AC: 7455 AN: 10564

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47867 AN: 67918

Other (OTH) AF: 0.740 AC: 1558 AN: 2106

Alfa AF: 0.715 Hom.: 168226

Bravo AF: 0.736

Asia WGS AF: 0.668 AC: 2322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.69
DANN	Benign	0.25
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4751178; hg19: chr10-131992245;