10-107810092-T-C

Variant names:

• chr10-107810092-T-C
• rs12570947
• ENST00000593666.6:n.492+44343A>G

Variant summary

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

The ENST00000593666.6(LINC01435):​n.492+44343A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,014 control chromosomes in the GnomAD database, including 3,805 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 0.21 (3805 hom., cov: 32)
• Consequence: LINC01435 ENST00000593666.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.905
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 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.492+44343A>G		intron_variant	Intron 4 of 4	5
LINC01435	ENST00000596263.5	n.385+2714A>G		intron_variant	Intron 3 of 3	5
LINC01435	ENST00000598903.5	n.364-49217A>G		intron_variant	Intron 3 of 4	5
LINC01435	ENST00000630847.2	n.525+43066A>G		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31449 AN: 151896 Hom.: 3793 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.207 AC: 31498 AN: 152014 Hom.: 3805 Cov.: 32 AF XY: 0.214 AC XY: 15901 AN XY: 74264

African (AFR) AF: 0.246 AC: 10202 AN: 41450

American (AMR) AF: 0.207 AC: 3168 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3466

East Asian (EAS) AF: 0.533 AC: 2727 AN: 5120

South Asian (SAS) AF: 0.332 AC: 1596 AN: 4814

European-Finnish (FIN) AF: 0.238 AC: 2514 AN: 10570

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10187 AN: 67998

Other (OTH) AF: 0.189 AC: 400 AN: 2112

Alfa AF: 0.156 Hom.: 2587

Bravo AF: 0.210

Asia WGS AF: 0.438 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.76
PhyloP100		-0.91
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12570947; hg19: chr10-109569850;