rs6549438

Variant names:

• chr3-72112082-T-A
• rs6549438
• ENST00000469218.6:n.149-12072A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-72112082-T-A
• chr3-72112082-T-C
• chr3-72112082-T-G

Variant summary

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

The ENST00000469218.6(LINC00877):​n.149-12072A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,128 control chromosomes in the GnomAD database, including 23,518 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 0.54 (23518 hom., cov: 33)
• Consequence: LINC00877 ENST00000469218.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 5 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00877	ENST00000469218.6	n.149-12072A>T		intron_variant	Intron 2 of 8	5
LINC00877	ENST00000481148.5	n.132-12072A>T		intron_variant	Intron 1 of 2	4
LINC00877	ENST00000626474.3	n.456-12072A>T		intron_variant	Intron 3 of 8	5

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82775 AN: 152010 Hom.: 23479 Cov.: 33

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.545 AC: 82865 AN: 152128 Hom.: 23518 Cov.: 33 AF XY: 0.545 AC XY: 40522 AN XY: 74388

African (AFR) AF: 0.678 AC: 28112 AN: 41492

American (AMR) AF: 0.469 AC: 7169 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1896 AN: 3470

East Asian (EAS) AF: 0.827 AC: 4294 AN: 5190

South Asian (SAS) AF: 0.545 AC: 2627 AN: 4822

European-Finnish (FIN) AF: 0.491 AC: 5189 AN: 10564

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31835 AN: 67982

Other (OTH) AF: 0.559 AC: 1177 AN: 2106

Alfa AF: 0.503 Hom.: 2409

Bravo AF: 0.553

Asia WGS AF: 0.667 AC: 2318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	16
DANN	Benign	0.79
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs6549438; hg19: chr3-72161233;