chr10-108149985-T-G

Variant names:

• chr10-108149985-T-G
• rs1936488
• ENST00000627225.2:n.165-38383A>C

Variant summary

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

The ENST00000627225.2(LINC01435):​n.165-38383A>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 1 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=-0.87).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01435	ENST00000627225.2	n.165-38383A>C		intron_variant	Intron 2 of 5	5
LINC01435	ENST00000629275.2	n.115-38383A>C		intron_variant	Intron 1 of 4	5
LINC01435	ENST00000631100.1	n.64+17921A>C		intron_variant	Intron 1 of 5	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

African (AFR) AF: 0.330 AC: 13657 AN: 41436

American (AMR) AF: 0.311 AC: 4744 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1922 AN: 3470

East Asian (EAS) AF: 0.192 AC: 994 AN: 5172

South Asian (SAS) AF: 0.378 AC: 1820 AN: 4820

European-Finnish (FIN) AF: 0.259 AC: 2735 AN: 10568

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21782 AN: 67966

Other (OTH) AF: 0.350 AC: 737 AN: 2108

Alfa AF: 0.337 Hom.: 13974

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
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs1936488; hg19: chr10-109909743;