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 ENST00000659487.2(ENSG00000287028):​n.216-309T>C 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: ENSG00000287028 ENST00000659487.2 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659487.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02550	ENST00000636877.1	TSL:5	n.838-5615A>G		intron	N/A
	ENSG00000287028	ENST00000659487.2		n.216-309T>C		intron	N/A
	LINC02550	ENST00000783537.1		n.388-5615A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs167685;

hg19: chr11-110968650;