rs3952812

chr3-194090244-C-G

Variant summary

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

The XR_007096295.1(LOC102724877):n.283-1263C>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 0.0875 in 152,212 control chromosomes in the GnomAD database, including 814 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 0.088 (814 hom., cov: 32)
• Consequence: LOC102724877 XR_007096295.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981

Genes affected

LOC102724877 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724877	XR_007096295.1	n.283-1263C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0876 AC: 13319 AN: 152094 Hom.: 817 Cov.: 32

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.0792

Gnomad FIN AF: 0.0972

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0893

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0875 AC: 13320 AN: 152212 Hom.: 814 Cov.: 32 AF XY: 0.0909 AC XY: 6763 AN XY: 74406

Gnomad4 AFR AF: 0.0374

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.0790

Gnomad4 FIN AF: 0.0972

Gnomad4 NFE AF: 0.0894

Gnomad4 OTH AF: 0.0870

Alfa AF: 0.0866 Hom.: 74

Bravo AF: 0.0872

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.043
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3952812; hg19: chr3-193808033;