rs4751178

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-130193981-A-G
• chr10-130193981-A-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902561	XM_047426136.1	c.*2756A>G		3_prime_UTR_variant	Exon 2 of 2		XP_047282092.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

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 v4.3

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;