chr3-157077679-A-G

Variant names:

• chr3-157077679-A-G
• rs13322435
• ENST00000782045.1:n.569-3476T>C

Variant summary

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

The ENST00000782045.1(LINC00880):​n.569-3476T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,048 control chromosomes in the GnomAD database, including 16,924 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 0.47 (16924 hom., cov: 32)
• Consequence: LINC00880 ENST00000782045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 23 publications found

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782045.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00880	ENST00000782045.1		n.569-3476T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70700 AN: 151930 Hom.: 16903 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.465 AC: 70759 AN: 152048 Hom.: 16924 Cov.: 32 AF XY: 0.464 AC XY: 34460 AN XY: 74324

African (AFR) AF: 0.535 AC: 22190 AN: 41456

American (AMR) AF: 0.463 AC: 7083 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1962 AN: 3468

East Asian (EAS) AF: 0.647 AC: 3343 AN: 5164

South Asian (SAS) AF: 0.534 AC: 2574 AN: 4818

European-Finnish (FIN) AF: 0.328 AC: 3467 AN: 10572

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28568 AN: 67966

Other (OTH) AF: 0.494 AC: 1042 AN: 2110

Alfa AF: 0.446 Hom.: 1930

Bravo AF: 0.478

Asia WGS AF: 0.573 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.30
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs13322435; hg19: chr3-156795468;