rs10520350

Variant names:

• chr4-176473042-C-G
• rs10520350
• XR_007058376.1:n.1157+22218C>G

Your query was ambiguous. Multiple possible variants found:

• chr4-176473042-C-G
• chr4-176473042-C-T

Variant summary

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

The XR_007058376.1(LOC124900817):​n.1157+22218C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.072 in 152,228 control chromosomes in the GnomAD database, including 422 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 0.072 (422 hom., cov: 33)
• Consequence: LOC124900817 XR_007058376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265
• Publications: 3 publications found

Genes affected

LOC124900817 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900817	XR_007058376.1	n.1157+22218C>G		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0720 AC: 10947 AN: 152110 Hom.: 421 Cov.: 33

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0592

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.0409

Gnomad SAS AF: 0.0609

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0847

Gnomad OTH AF: 0.0508

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

GnomAD4 genome AF: 0.0720 AC: 10968 AN: 152228 Hom.: 422 Cov.: 33 AF XY: 0.0693 AC XY: 5156 AN XY: 74408

African (AFR) AF: 0.0698 AC: 2901 AN: 41544

American (AMR) AF: 0.0590 AC: 903 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 130 AN: 3470

East Asian (EAS) AF: 0.0410 AC: 213 AN: 5192

South Asian (SAS) AF: 0.0612 AC: 295 AN: 4820

European-Finnish (FIN) AF: 0.0562 AC: 595 AN: 10584

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

European-Non Finnish (NFE) AF: 0.0847 AC: 5762 AN: 68006

Other (OTH) AF: 0.0498 AC: 105 AN: 2110

Alfa AF: 0.0385 Hom.: 28

Bravo AF: 0.0724

Asia WGS AF: 0.0490 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.4
DANN	Benign	0.51
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs10520350; hg19: chr4-177394193;