rs1402704

Variant names:

• chr11-76228556-G-A
• rs1402704
• ENST00000724887.1:n.245+8065C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-76228556-G-A
• chr11-76228556-G-C

Variant summary

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

The ENST00000724887.1(LINC02761):​n.245+8065C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,166 control chromosomes in the GnomAD database, including 7,856 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 0.32 (7856 hom., cov: 33)
• Consequence: LINC02761 ENST00000724887.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 6 publications found

Genes affected

LINC02761 (HGNC:54281): (long intergenic non-protein coding RNA 2761)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 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
LINC02761	ENST00000724887.1	n.245+8065C>T		intron_variant	Intron 1 of 2
LINC02761	ENST00000724888.1	n.238+8072C>T		intron_variant	Intron 1 of 2
LINC02761	ENST00000724889.1	n.249+8061C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48916 AN: 152048 Hom.: 7860 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.322 AC: 48923 AN: 152166 Hom.: 7856 Cov.: 33 AF XY: 0.324 AC XY: 24091 AN XY: 74398

African (AFR) AF: 0.303 AC: 12581 AN: 41522

American (AMR) AF: 0.328 AC: 5022 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1109 AN: 3464

East Asian (EAS) AF: 0.417 AC: 2155 AN: 5168

South Asian (SAS) AF: 0.322 AC: 1553 AN: 4824

European-Finnish (FIN) AF: 0.335 AC: 3549 AN: 10594

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22017 AN: 67986

Other (OTH) AF: 0.320 AC: 675 AN: 2108

Alfa AF: 0.320 Hom.: 24894

Bravo AF: 0.320

Asia WGS AF: 0.361 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.28
DANN	Benign	0.88
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1402704; hg19: chr11-75939600;