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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906112	XR_007088012.1	n.229-70507C>A		intron_variant	Intron 1 of 2
LOC124906112	XR_007088015.1	n.229-70507C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;