rs4751178

chr10-130193981-A-Gchr10-130193981-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124902561 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902561	XM_047426136.1	c.*2756A>G		3_prime_UTR_variant	2/2

Ensembl

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

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

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.740

Alfa AF: 0.711 Hom.: 80809

Bravo AF: 0.736

Asia WGS AF: 0.668 AC: 2322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.69
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4751178; hg19: chr10-131992245;