rs2252004

Variant names:

• chr10-121085195-C-A
• rs2252004
• XR_007062319.1:n.512G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-121085195-C-A
• chr10-121085195-C-G
• chr10-121085195-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 26 publications found

Genes affected

LOC124902516 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124902516	XR_007062319.1	n.512G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.518 AC: 21483 AN: 41480

American (AMR) AF: 0.287 AC: 4393 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0870 AC: 302 AN: 3470

East Asian (EAS) AF: 0.292 AC: 1512 AN: 5182

South Asian (SAS) AF: 0.334 AC: 1610 AN: 4826

European-Finnish (FIN) AF: 0.137 AC: 1448 AN: 10608

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0946 AC: 6435 AN: 68004

Other (OTH) AF: 0.198 AC: 418 AN: 2112

Alfa AF: 0.152 Hom.: 6807

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2252004; hg19: chr10-122844709;