rs922556

Variant names:

• chr5-124210411-T-C
• rs922556
• ENST00000628324.2:n.403-147901A>G

Variant summary

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

The ENST00000628324.2(LINC01170):​n.403-147901A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,050 control chromosomes in the GnomAD database, including 18,498 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 0.43 (18498 hom., cov: 32)
• Consequence: LINC01170 ENST00000628324.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439
• Publications: 4 publications found

Genes affected

LINC01170 (HGNC:49542): (long intergenic non-protein coding RNA 1170)

ENSG00000297714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01170	NR_125774.1	n.490-147901A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01170	ENST00000628324.2	n.403-147901A>G		intron_variant	Intron 2 of 3	2
LINC01170	ENST00000653233.2	n.500-73091A>G		intron_variant	Intron 3 of 6
LINC01170	ENST00000657766.2	n.394-73091A>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66020 AN: 151932 Hom.: 18439 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.435 AC: 66134 AN: 152050 Hom.: 18498 Cov.: 32 AF XY: 0.429 AC XY: 31902 AN XY: 74326

African (AFR) AF: 0.806 AC: 33403 AN: 41448

American (AMR) AF: 0.320 AC: 4887 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1350 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1888 AN: 5154

South Asian (SAS) AF: 0.393 AC: 1893 AN: 4820

European-Finnish (FIN) AF: 0.233 AC: 2461 AN: 10578

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.279 AC: 18969 AN: 67986

Other (OTH) AF: 0.404 AC: 855 AN: 2114

Alfa AF: 0.326 Hom.: 5492

Bravo AF: 0.459

Asia WGS AF: 0.421 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.81
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs922556; hg19: chr5-123546104;