rs1931605

Positions:

• chr10-108030075-G-T

Variant summary

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

The NR_125760.1(LINC01435):​n.543+10286C>A 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 0.527 in 151,960 control chromosomes in the GnomAD database, including 23,712 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 0.53 (23712 hom., cov: 32)
• Consequence: LINC01435 NR_125760.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01435	NR_125760.1	n.543+10286C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01435	ENST00000630847.2	n.194+10286C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80029 AN: 151842 Hom.: 23652 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.527 AC: 80133 AN: 151960 Hom.: 23712 Cov.: 32 AF XY: 0.519 AC XY: 38509 AN XY: 74258

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.507

Alfa AF: 0.492 Hom.: 2981

Bravo AF: 0.548

Asia WGS AF: 0.323 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1931605; hg19: chr10-109789833;