rs6572335

Variant names:

• chr14-45965382-A-G
• rs6572335
• ENST00000555246.5:n.76+24364A>G

Variant summary

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

The ENST00000555246.5(LINC00871):​n.76+24364A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 150,898 control chromosomes in the GnomAD database, including 12,666 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 0.38 (12666 hom., cov: 31)
• Consequence: LINC00871 ENST00000555246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 2 publications found

Genes affected

LINC00871 (HGNC:47038): (long intergenic non-protein coding RNA 871)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 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
LINC00871	ENST00000555246.5	n.76+24364A>G		intron_variant	Intron 1 of 5	5
LINC00871	ENST00000664642.1	n.185+24364A>G		intron_variant	Intron 2 of 5
LINC00871	ENST00000666179.1	n.176+24364A>G		intron_variant	Intron 2 of 4
LINC00871	ENST00000761148.1	n.179+24364A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.385 AC: 57978 AN: 150780 Hom.: 12656 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.384 AC: 58003 AN: 150898 Hom.: 12666 Cov.: 31 AF XY: 0.382 AC XY: 28142 AN XY: 73662

African (AFR) AF: 0.182 AC: 7499 AN: 41300

American (AMR) AF: 0.387 AC: 5849 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1535 AN: 3436

East Asian (EAS) AF: 0.247 AC: 1257 AN: 5084

South Asian (SAS) AF: 0.383 AC: 1844 AN: 4812

European-Finnish (FIN) AF: 0.464 AC: 4886 AN: 10532

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33493 AN: 67330

Other (OTH) AF: 0.411 AC: 858 AN: 2090

Alfa AF: 0.410 Hom.: 2386

Bravo AF: 0.370

Asia WGS AF: 0.311 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6572335; hg19: chr14-46434585;