chr2-200033174-T-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906112	XR_007088012.1	n.229-22278A>G		intron_variant	Intron 1 of 2
LOC124906112	XR_007088015.1	n.229-22278A>G		intron_variant	Intron 1 of 2

Ensembl

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

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 v4.3

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;