rs4532099

Positions:

• chr3-72266805-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000626474.3(LINC00877):​n.358+8303A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 149,218 control chromosomes in the GnomAD database, including 49,847 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 0.81 (49847 hom., cov: 25)
• Consequence: LINC00877 ENST00000626474.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

Genes affected

LINC00877 (HGNC:27706): (long intergenic non-protein coding RNA 877)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00877	ENST00000626474.3	n.358+8303A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.814 AC: 121437 AN: 149102 Hom.: 49804 Cov.: 25

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.735

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.814 AC: 121537 AN: 149218 Hom.: 49847 Cov.: 25 AF XY: 0.816 AC XY: 59264 AN XY: 72596

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.796

Alfa AF: 0.768 Hom.: 94947

Bravo AF: 0.816

Asia WGS AF: 0.791 AC: 2695 AN: 3406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4532099; hg19: chr3-72315956;