10-112927046-T-C

Position:

• chr10-112927046-T-C

Variant summary

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

The XR_001747706.2(LINC02935):​n.279-83T>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 0.49 in 152,052 control chromosomes in the GnomAD database, including 18,786 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 0.49 (18786 hom., cov: 32)
• Consequence: LINC02935 XR_001747706.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

LINC02935 (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 (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02935	XR_001747706.2	n.279-83T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74469 AN: 151934 Hom.: 18764 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.490 AC: 74536 AN: 152052 Hom.: 18786 Cov.: 32 AF XY: 0.483 AC XY: 35878 AN XY: 74342

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.0655

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.509

Alfa AF: 0.503 Hom.: 39648

Bravo AF: 0.488

Asia WGS AF: 0.269 AC: 936 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	3.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11196152; hg19: chr10-114686805;