rs10497847

Variant names:

• chr2-200081403-G-T
• rs10497847
• XR_007088012.1:n.229-70507C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007088012.1(LOC124906112):​n.229-70507C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,114 control chromosomes in the GnomAD database, including 2,299 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 0.17 (2299 hom., cov: 32)
• Consequence: LOC124906112 XR_007088012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.736
• Publications: 2 publications found

Genes affected

LOC124906112 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.188 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: 0.170 AC: 25857 AN: 151996 Hom.: 2298 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.170 AC: 25882 AN: 152114 Hom.: 2299 Cov.: 32 AF XY: 0.167 AC XY: 12451 AN XY: 74354

African (AFR) AF: 0.154 AC: 6377 AN: 41492

American (AMR) AF: 0.194 AC: 2966 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 694 AN: 3468

East Asian (EAS) AF: 0.107 AC: 554 AN: 5156

South Asian (SAS) AF: 0.169 AC: 813 AN: 4810

European-Finnish (FIN) AF: 0.144 AC: 1522 AN: 10570

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12136 AN: 67998

Other (OTH) AF: 0.198 AC: 418 AN: 2114

Alfa AF: 0.182 Hom.: 9533

Bravo AF: 0.177

Asia WGS AF: 0.145 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	15
DANN	Benign	0.78
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs10497847; hg19: chr2-200946126;