10-130121896-C-T

Variant names:

• chr10-130121896-C-T
• rs1536087
• XR_007062392.1:n.189G>A

Variant summary

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

The XR_007062392.1(LOC124902560):​n.189G>A 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 0.417 in 152,070 control chromosomes in the GnomAD database, including 13,576 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 0.42 (13576 hom., cov: 33)
• Consequence: LOC124902560 XR_007062392.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 5 publications found

Genes affected

LOC124902560 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902560	XR_007062392.1	n.189G>A		non_coding_transcript_exon_variant	Exon 1 of 2
LOC102724883	NR_188169.1	n.890-4358C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300559	ENST00000772721.1	n.797-1643G>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63402 AN: 151952 Hom.: 13551 Cov.: 33

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.417 AC: 63469 AN: 152070 Hom.: 13576 Cov.: 33 AF XY: 0.428 AC XY: 31827 AN XY: 74326

African (AFR) AF: 0.397 AC: 16447 AN: 41478

American (AMR) AF: 0.492 AC: 7509 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3468

East Asian (EAS) AF: 0.679 AC: 3489 AN: 5142

South Asian (SAS) AF: 0.482 AC: 2321 AN: 4820

European-Finnish (FIN) AF: 0.485 AC: 5143 AN: 10602

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.380 AC: 25850 AN: 67968

Other (OTH) AF: 0.438 AC: 925 AN: 2114

Alfa AF: 0.388 Hom.: 5935

Bravo AF: 0.420

Asia WGS AF: 0.575 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1536087; hg19: chr10-131920160;