rs1936488

Positions:

• chr10-108149985-T-G

Variant summary

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

The ENST00000627225.2(LINC01435):​n.165-38383A>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 0.322 in 151,980 control chromosomes in the GnomAD database, including 8,028 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 0.32 (8028 hom., cov: 32)
• Consequence: LINC01435 ENST00000627225.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.363 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	ENST00000627225.2	n.165-38383A>C		intron_variant, non_coding_transcript_variant		5
LINC01435	ENST00000629275.2	n.115-38383A>C		intron_variant, non_coding_transcript_variant		5
LINC01435	ENST00000631100.1	n.64+17921A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48854 AN: 151864 Hom.: 8008 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.322 AC: 48902 AN: 151980 Hom.: 8028 Cov.: 32 AF XY: 0.320 AC XY: 23742 AN XY: 74282

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.350

Alfa AF: 0.337 Hom.: 11996

Bravo AF: 0.328

Asia WGS AF: 0.288 AC: 1000 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1936488; hg19: chr10-109909743;