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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;