chr10-107799143-C-G

Variant names:

• chr10-107799143-C-G
• rs10509846
• ENST00000593666.6:n.493-38268G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000593666.6(LINC01435):​n.493-38268G>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 ENST00000593666.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000593666.6	n.493-38268G>C		intron_variant	Intron 4 of 4	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

African (AFR) AF: 0.0634 AC: 2633 AN: 41502

American (AMR) AF: 0.130 AC: 1984 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 127 AN: 3466

East Asian (EAS) AF: 0.126 AC: 654 AN: 5172

South Asian (SAS) AF: 0.141 AC: 679 AN: 4824

European-Finnish (FIN) AF: 0.0514 AC: 544 AN: 10586

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0302 AC: 2052 AN: 67994

Other (OTH) AF: 0.0659 AC: 139 AN: 2110

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
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs10509846; hg19: chr10-109558901;