rs2102313

Variant names:

• chr3-71977675-G-A
• rs2102313
• ENST00000666244.1:n.1223-3701C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-71977675-G-A
• chr3-71977675-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.1223-3701C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,054 control chromosomes in the GnomAD database, including 8,689 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 0.33 (8689 hom., cov: 32)
• Consequence: LINC00877 ENST00000666244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 4 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=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 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.1223-3701C>T		intron_variant	Intron 5 of 6
LINC00877	ENST00000811845.1	n.298-816C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50121 AN: 151936 Hom.: 8678 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.330 AC: 50158 AN: 152054 Hom.: 8689 Cov.: 32 AF XY: 0.336 AC XY: 25002 AN XY: 74318

African (AFR) AF: 0.229 AC: 9510 AN: 41484

American (AMR) AF: 0.355 AC: 5418 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1060 AN: 3466

East Asian (EAS) AF: 0.500 AC: 2582 AN: 5162

South Asian (SAS) AF: 0.465 AC: 2241 AN: 4820

European-Finnish (FIN) AF: 0.402 AC: 4247 AN: 10556

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 24005 AN: 67970

Other (OTH) AF: 0.338 AC: 714 AN: 2110

Alfa AF: 0.344 Hom.: 33290

Bravo AF: 0.322

Asia WGS AF: 0.448 AC: 1555 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.8
DANN	Benign	0.56
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2102313; hg19: chr3-72026826;