rs10497845

Variant names:

• chr2-200033174-T-C
• rs10497845
• XR_007088012.1:n.229-22278A>G

Variant summary

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

The XR_007088012.1(LOC124906112):​n.229-22278A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0787 in 152,124 control chromosomes in the GnomAD database, including 832 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 0.079 (832 hom., cov: 31)
• Consequence: LOC124906112 XR_007088012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 2 publications found

Genes affected

LOC124906112 (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 (AMR) allele frequency at 95% confidence interval = 0.22 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: 0.0786 AC: 11950 AN: 152006 Hom.: 823 Cov.: 31

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0563

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.0801

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

GnomAD4 genome AF: 0.0787 AC: 11978 AN: 152124 Hom.: 832 Cov.: 31 AF XY: 0.0829 AC XY: 6166 AN XY: 74360

African (AFR) AF: 0.0975 AC: 4048 AN: 41502

American (AMR) AF: 0.226 AC: 3458 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 127 AN: 3466

East Asian (EAS) AF: 0.149 AC: 772 AN: 5174

South Asian (SAS) AF: 0.0561 AC: 269 AN: 4794

European-Finnish (FIN) AF: 0.0690 AC: 731 AN: 10596

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0348 AC: 2369 AN: 68008

Other (OTH) AF: 0.0787 AC: 166 AN: 2108

Alfa AF: 0.0705 Hom.: 233

Bravo AF: 0.0966

Asia WGS AF: 0.0980 AC: 342 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	1.1
DANN	Benign	0.69
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10497845; hg19: chr2-200897897;