rs765651

Variant names:

• chr10-107849542-A-G
• rs765651
• ENST00000593666.6:n.492+4893T>C

Variant summary

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

The ENST00000593666.6(LINC01435):​n.492+4893T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 148,118 control chromosomes in the GnomAD database, including 4,493 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 0.24 (4493 hom., cov: 32)
• Consequence: LINC01435 ENST00000593666.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 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+4893T>C		intron_variant	Intron 4 of 4	5
LINC01435	ENST00000594566.5	n.456-4873T>C		intron_variant	Intron 4 of 4	5
LINC01435	ENST00000596263.5	n.285-36636T>C		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.243 AC: 35968 AN: 148006 Hom.: 4480 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.0834

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.243 AC: 36007 AN: 148118 Hom.: 4493 Cov.: 32 AF XY: 0.238 AC XY: 17138 AN XY: 72092

African (AFR) AF: 0.197 AC: 8153 AN: 41298

American (AMR) AF: 0.197 AC: 2796 AN: 14222

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1276 AN: 3448

East Asian (EAS) AF: 0.0835 AC: 364 AN: 4358

South Asian (SAS) AF: 0.206 AC: 908 AN: 4408

European-Finnish (FIN) AF: 0.211 AC: 2152 AN: 10194

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.292 AC: 19540 AN: 66956

Other (OTH) AF: 0.238 AC: 488 AN: 2048

Alfa AF: 0.271 Hom.: 24281

Bravo AF: 0.231

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.61
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs765651; hg19: chr10-109609300;