rs10520350

chr4-176473042-C-Gchr4-176473042-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058376.1(LOC124900817):n.1157+22218C>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265

Genes affected

LOC124900817 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124900817	XR_007058376.1	n.1157+22218C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0698

Gnomad4 AMR AF: 0.0590

Gnomad4 ASJ AF: 0.0375

Gnomad4 EAS AF: 0.0410

Gnomad4 SAS AF: 0.0612

Gnomad4 FIN AF: 0.0562

Gnomad4 NFE AF: 0.0847

Gnomad4 OTH AF: 0.0498

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520350; hg19: chr4-177394193;