rs10510634

Positions:

• chr3-30305477-A-G

Variant summary

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

The XR_007095854.1(LOC124909358):​n.1269A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,222 control chromosomes in the GnomAD database, including 1,919 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 0.16 (1919 hom., cov: 32)
• Consequence: LOC124909358 XR_007095854.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80

Genes affected

LOC124909358 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124909358	XR_007095854.1	n.1269A>G		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23873 AN: 152104 Hom.: 1919 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.157 AC: 23871 AN: 152222 Hom.: 1919 Cov.: 32 AF XY: 0.153 AC XY: 11406 AN XY: 74426

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.157

Alfa AF: 0.176 Hom.: 1372

Bravo AF: 0.152

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510634; hg19: chr3-30346968;