rs2252004

chr10-121085195-C-A

Variant summary

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

The XR_007062319.1(LOC124902516):n.512G>T 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 0.247 in 152,182 control chromosomes in the GnomAD database, including 7,260 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 0.25 (7260 hom., cov: 33)
• Consequence: LOC124902516 XR_007062319.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573

Genes affected

LOC124902516 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902516	XR_007062319.1	n.512G>T		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37555 AN: 152064 Hom.: 7218 Cov.: 33

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.0870

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0946

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.247 AC: 37654 AN: 152182 Hom.: 7260 Cov.: 33 AF XY: 0.254 AC XY: 18886 AN XY: 74426

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.0870

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.0946

Gnomad4 OTH AF: 0.198

Alfa AF: 0.146 Hom.: 1688

Bravo AF: 0.267

Asia WGS AF: 0.340 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.3
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2252004; hg19: chr10-122844709;