rs1324705

Variant names:

• chr10-89883850-C-T
• rs1324705
• ENST00000629067.2:n.626+29843C>T

Variant summary

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

The ENST00000629067.2(LINC00865):​n.626+29843C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,690 control chromosomes in the GnomAD database, including 25,447 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 0.56 (25447 hom., cov: 31)
• Consequence: LINC00865 ENST00000629067.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 1 publications found

Genes affected

LINC00865 (HGNC:45170): (long intergenic non-protein coding RNA 865)

LINC01374 (HGNC:50631): (long intergenic non-protein coding RNA 1374)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01374	NR_149080.1	n.102+29843C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00865	ENST00000629067.2	n.626+29843C>T		intron_variant	Intron 2 of 2	3
LINC00865	ENST00000664430.1	n.413+29843C>T		intron_variant	Intron 1 of 3
LINC00865	ENST00000715760.1	n.605+29843C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85168 AN: 151570 Hom.: 25386 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.562 AC: 85299 AN: 151690 Hom.: 25447 Cov.: 31 AF XY: 0.557 AC XY: 41240 AN XY: 74096

African (AFR) AF: 0.754 AC: 31217 AN: 41414

American (AMR) AF: 0.610 AC: 9272 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1903 AN: 3462

East Asian (EAS) AF: 0.371 AC: 1903 AN: 5132

South Asian (SAS) AF: 0.616 AC: 2969 AN: 4816

European-Finnish (FIN) AF: 0.337 AC: 3546 AN: 10534

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32679 AN: 67836

Other (OTH) AF: 0.571 AC: 1199 AN: 2100

Alfa AF: 0.535 Hom.: 8837

Bravo AF: 0.588

Asia WGS AF: 0.556 AC: 1934 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.72
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1324705; hg19: chr10-91643607;