rs2505089

chr10-30116476-A-Cchr10-30116476-A-Gchr10-30116476-A-T

Variant summary

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

The XR_001747405.2(LOC101929256):n.490-4567A>C 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 0.816 in 152,162 control chromosomes in the GnomAD database, including 51,138 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 0.82 (51138 hom., cov: 32)
• Consequence: LOC101929256 XR_001747405.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

Genes affected

LOC101929256 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929256	XR_001747405.2	n.490-4567A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124080 AN: 152044 Hom.: 51105 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.816 AC: 124166 AN: 152162 Hom.: 51138 Cov.: 32 AF XY: 0.814 AC XY: 60596 AN XY: 74402

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.876

Gnomad4 ASJ AF: 0.892

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.825

Alfa AF: 0.846 Hom.: 11595

Bravo AF: 0.819

Asia WGS AF: 0.706 AC: 2456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.4
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2505089; hg19: chr10-30405405;