rs167685

Variant names:

• chr11-111097926-T-C
• rs167685
• ENST00000636877.1:n.838-5615A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-111097926-T-C
• chr11-111097926-T-G

Variant summary

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

The ENST00000636877.1(LINC02550):​n.838-5615A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,922 control chromosomes in the GnomAD database, including 10,954 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 0.37 (10954 hom., cov: 32)
• Consequence: LINC02550 ENST00000636877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 0 publications found

Genes affected

LINC02550 (HGNC:53585): (long intergenic non-protein coding RNA 2550)

ENSG00000287028 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723966	XR_428993.4	n.208-309T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02550	ENST00000636877.1	n.838-5615A>G		intron_variant	Intron 3 of 3	5
ENSG00000287028	ENST00000659487.2	n.216-309T>C		intron_variant	Intron 1 of 2
LINC02550	ENST00000783537.1	n.388-5615A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56806 AN: 151804 Hom.: 10921 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.374 AC: 56874 AN: 151922 Hom.: 10954 Cov.: 32 AF XY: 0.375 AC XY: 27829 AN XY: 74252

African (AFR) AF: 0.435 AC: 18004 AN: 41410

American (AMR) AF: 0.466 AC: 7113 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3466

East Asian (EAS) AF: 0.355 AC: 1830 AN: 5160

South Asian (SAS) AF: 0.314 AC: 1513 AN: 4816

European-Finnish (FIN) AF: 0.274 AC: 2889 AN: 10558

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23394 AN: 67934

Other (OTH) AF: 0.369 AC: 778 AN: 2108

Alfa AF: 0.350 Hom.: 1196

Bravo AF: 0.394

Asia WGS AF: 0.356 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.77
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs167685; hg19: chr11-110968650;