rs10509846

chr10-107799143-C-Gchr10-107799143-C-T

Variant summary

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

The ENST00000630847.2(LINC01435):n.525+54015G>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 0.0585 in 152,148 control chromosomes in the GnomAD database, including 375 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 0.058 (375 hom., cov: 32)
• Consequence: LINC01435 ENST00000630847.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01435	ENST00000630847.2	n.525+54015G>C		intron_variant, non_coding_transcript_variant		5
LINC01435	ENST00000593666.5	n.334-38268G>C		intron_variant, non_coding_transcript_variant		5
LINC01435	ENST00000598903.5	n.364-38268G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0585 AC: 8891 AN: 152030 Hom.: 376 Cov.: 32

Gnomad AFR AF: 0.0635

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0514

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0302

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0585 AC: 8896 AN: 152148 Hom.: 375 Cov.: 32 AF XY: 0.0633 AC XY: 4711 AN XY: 74372

Gnomad4 AFR AF: 0.0634

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.0366

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0514

Gnomad4 NFE AF: 0.0302

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.00888 Hom.: 3

Bravo AF: 0.0622

Asia WGS AF: 0.123 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.28
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509846; hg19: chr10-109558901;