rs2901286

Variant names:

• chr10-121141109-C-A
• rs2901286
• XR_007062317.1:n.168-21760G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_946379.3(LOC105378522):​n.357-10939C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0205 in 152,290 control chromosomes in the GnomAD database, including 149 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 0.021 (149 hom., cov: 33)
• Consequence: LOC105378522 XR_946379.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.827

Genes affected

LOC124902515 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902515	XR_007062317.1	n.168-21760G>T		intron_variant	Intron 1 of 1
LOC124902515	XR_007062318.1	n.159-21760G>T		intron_variant	Intron 1 of 1
LOC105378522	XR_946379.3	n.357-10939C>A		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0205 AC: 3123 AN: 152172 Hom.: 149 Cov.: 33

Gnomad AFR AF: 0.00374

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0246

Gnomad FIN AF: 0.0247

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0205 AC: 3128 AN: 152290 Hom.: 149 Cov.: 33 AF XY: 0.0232 AC XY: 1728 AN XY: 74462

Gnomad4 AFR AF: 0.00373

Gnomad4 AMR AF: 0.0467

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.0246

Gnomad4 FIN AF: 0.0247

Gnomad4 NFE AF: 0.0108

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0204 Hom.: 196

Bravo AF: 0.0232

Asia WGS AF: 0.0790 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2901286; hg19: chr10-122900623;