rs7624327

Positions:

• chr3-157119117-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC00880 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00880	NR_034007.1	n.127+3759C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00880	ENST00000471357.1	n.129+3759C>T		intron_variant		1
LINC00880	ENST00000659739.1	n.290+3759C>T		intron_variant
LINC00881	ENST00000665438.1	n.305-14925G>A		intron_variant

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

Gnomad4 AFR AF: 0.0571

Gnomad4 AMR AF: 0.0721

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.0711

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.100

Alfa AF: 0.103 Hom.: 534

Bravo AF: 0.0863

Asia WGS AF: 0.211 AC: 732 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7624327; hg19: chr3-156836906;