rs10509966

chr10-112916421-A-G

Variant summary

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

The XR_001747706.2(LINC02935):n.278+10208A>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 0.193 in 152,156 control chromosomes in the GnomAD database, including 3,506 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 0.19 (3506 hom., cov: 31)
• Consequence: LINC02935 XR_001747706.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387

Genes affected

LINC02935 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02935	XR_001747706.2	n.278+10208A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29330 AN: 152038 Hom.: 3502 Cov.: 31

Gnomad AFR AF: 0.0545

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0492

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.193 AC: 29341 AN: 152156 Hom.: 3506 Cov.: 31 AF XY: 0.191 AC XY: 14183 AN XY: 74362

Gnomad4 AFR AF: 0.0545

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.0495

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.207

Alfa AF: 0.228 Hom.: 672

Bravo AF: 0.185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.1
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: rs10509966; hg19: chr10-114676180;