rs12510781

Variant names:

• chr4-114719425-A-G
• rs12510781
• XR_007058238.1:n.221-1629T>C

Variant summary

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

The XR_007058238.1(LOC124900763):​n.221-1629T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0605 in 152,246 control chromosomes in the GnomAD database, including 381 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 0.061 (381 hom., cov: 32)
• Consequence: LOC124900763 XR_007058238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 3 publications found

Genes affected

LOC124900763 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900763	XR_007058238.1	n.221-1629T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0605 AC: 9206 AN: 152128 Hom.: 381 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0672

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0605 AC: 9211 AN: 152246 Hom.: 381 Cov.: 32 AF XY: 0.0590 AC XY: 4391 AN XY: 74448

African (AFR) AF: 0.105 AC: 4374 AN: 41550

American (AMR) AF: 0.0673 AC: 1030 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3470

East Asian (EAS) AF: 0.138 AC: 714 AN: 5172

South Asian (SAS) AF: 0.0588 AC: 284 AN: 4826

European-Finnish (FIN) AF: 0.0107 AC: 113 AN: 10608

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0333 AC: 2262 AN: 68004

Other (OTH) AF: 0.0687 AC: 145 AN: 2110

Alfa AF: 0.0434 Hom.: 349

Bravo AF: 0.0695

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.3
DANN	Benign	0.74
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs12510781; hg19: chr4-115640581;