rs1834180

Positions:

• chr10-107866308-G-A
• chr10-107866308-G-C
• chr10-107866308-G-T

Variant summary

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

The ENST00000630847.2(LINC01435):​n.274-11825C>T 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 0.733 in 151,672 control chromosomes in the GnomAD database, including 41,416 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 0.73 (41416 hom., cov: 29)
• Consequence: LINC01435 ENST00000630847.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 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.274-11825C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111093 AN: 151554 Hom.: 41351 Cov.: 29

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.733 AC: 111218 AN: 151672 Hom.: 41416 Cov.: 29 AF XY: 0.734 AC XY: 54373 AN XY: 74046

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.707

Alfa AF: 0.725 Hom.: 5782

Bravo AF: 0.747

Asia WGS AF: 0.845 AC: 2940 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1834180; hg19: chr10-109626066;