rs2135319

Variant names:

• chr3-71974549-G-A
• rs2135319
• ENST00000666244.1:n.1223-575C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-71974549-G-A
• chr3-71974549-G-C
• chr3-71974549-G-T

Variant summary

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

The ENST00000666244.1(LINC00877):​n.1223-575C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0911 in 152,076 control chromosomes in the GnomAD database, including 650 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 0.091 (650 hom., cov: 32)
• Consequence: LINC00877 ENST00000666244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 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	ENST00000666244.1	n.1223-575C>T		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13845 AN: 151958 Hom.: 649 Cov.: 32

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0909

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.0911 AC: 13849 AN: 152076 Hom.: 650 Cov.: 32 AF XY: 0.0898 AC XY: 6677 AN XY: 74352

African (AFR) AF: 0.0861 AC: 3568 AN: 41450

American (AMR) AF: 0.0833 AC: 1273 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3470

East Asian (EAS) AF: 0.191 AC: 983 AN: 5160

South Asian (SAS) AF: 0.105 AC: 506 AN: 4824

European-Finnish (FIN) AF: 0.0542 AC: 574 AN: 10584

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0909 AC: 6181 AN: 67982

Other (OTH) AF: 0.0946 AC: 200 AN: 2114

Alfa AF: 0.0928 Hom.: 1197

Bravo AF: 0.0937

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.59
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2135319; hg19: chr3-72023700;