3-157119117-G-A

Variant names:

• chr3-157119117-G-A
• rs7624327
• ENST00000471357.1:n.129+3759C>T

Variant summary

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

The ENST00000471357.1(LINC00880):​n.129+3759C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.093 in 152,108 control chromosomes in the GnomAD database, including 795 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 0.093 (795 hom., cov: 31)
• Consequence: LINC00880 ENST00000471357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 13 publications found

Genes affected

LINC00880 (HGNC:27948): (long intergenic non-protein coding RNA 880)

LINC00881 (HGNC:48567): (long intergenic non-protein coding RNA 881)

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 (SAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000471357.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00880	NR_034007.1		n.127+3759C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00880	ENST00000471357.1	TSL:1	n.129+3759C>T		intron	N/A
	LINC00880	ENST00000659739.1		n.290+3759C>T		intron	N/A
	LINC00881	ENST00000665438.2		n.314-14925G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14145 AN: 151988 Hom.: 795 Cov.: 31

Gnomad AFR AF: 0.0572

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.0722

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.0711

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0930 AC: 14143 AN: 152108 Hom.: 795 Cov.: 31 AF XY: 0.0938 AC XY: 6974 AN XY: 74346

African (AFR) AF: 0.0571 AC: 2371 AN: 41488

American (AMR) AF: 0.0721 AC: 1102 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3464

East Asian (EAS) AF: 0.142 AC: 735 AN: 5188

South Asian (SAS) AF: 0.283 AC: 1364 AN: 4820

European-Finnish (FIN) AF: 0.0711 AC: 751 AN: 10570

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7038 AN: 67978

Other (OTH) AF: 0.100 AC: 212 AN: 2112

Alfa AF: 0.0954 Hom.: 771

Bravo AF: 0.0863

Asia WGS AF: 0.211 AC: 732 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.61
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs7624327; hg19: chr3-156836906;