rs10509846

Variant names:

• chr10-107799143-C-G
• rs10509846
• ENST00000593666.5:n.334-38268G>C

Your query was ambiguous. Multiple possible variants found:

• chr10-107799143-C-G
• chr10-107799143-C-T

Variant summary

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

The ENST00000593666.5(LINC01435):​n.334-38268G>C variant causes a intron 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 ENST00000593666.5 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01435	ENST00000593666.5	n.334-38268G>C		intron_variant	Intron 3 of 3	5
LINC01435	ENST00000598903.5	n.364-38268G>C		intron_variant	Intron 3 of 4	5
LINC01435	ENST00000630847.2	n.525+54015G>C		intron_variant	Intron 5 of 5	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;