10-107849542-A-G

Position:

• chr10-107849542-A-G

Variant summary

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

The ENST00000630847.2(LINC01435):​n.525+3616T>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 0.243 in 148,118 control chromosomes in the GnomAD database, including 4,493 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 0.24 (4493 hom., cov: 32)
• Consequence: LINC01435 ENST00000630847.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199

Genes affected

LINC01435 (HGNC:50753): (long intergenic non-protein coding RNA 1435)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01435	ENST00000630847.2	n.525+3616T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.243 AC: 35968 AN: 148006 Hom.: 4480 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.0834

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.243 AC: 36007 AN: 148118 Hom.: 4493 Cov.: 32 AF XY: 0.238 AC XY: 17138 AN XY: 72092

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.0835

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.238

Alfa AF: 0.276 Hom.: 12217

Bravo AF: 0.231

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
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: rs765651; hg19: chr10-109609300;