chr22-34767787-C-T

Variant names:

• chr22-34767787-C-T
• rs18478
• XR_938204.3:n.7126C>T

Variant summary

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

The XR_938204.3(LOC105373014):​n.7126C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.086 in 152,166 control chromosomes in the GnomAD database, including 674 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 0.086 (674 hom., cov: 32)
• Consequence: LOC105373014 XR_938204.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 3 publications found

Genes affected

LOC105373014 (HGNC:):

LINC02885 (HGNC:41188): (long intergenic non-protein coding RNA 2885)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373014	XR_938204.3	n.7126C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02885	NR_138042.1	n.461-7300G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02885	ENST00000668433.1	n.344-8726G>A		intron_variant	Intron 3 of 3
LINC02885	ENST00000801714.1	n.35-7300G>A		intron_variant	Intron 1 of 2
LINC02885	ENST00000801715.1	n.35-7300G>A		intron_variant	Intron 1 of 2
LINC02885	ENST00000801716.1	n.31-7300G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0859 AC: 13066 AN: 152046 Hom.: 668 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0684

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.0523

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.0860 AC: 13091 AN: 152166 Hom.: 674 Cov.: 32 AF XY: 0.0849 AC XY: 6318 AN XY: 74384

African (AFR) AF: 0.111 AC: 4590 AN: 41534

American (AMR) AF: 0.0682 AC: 1042 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3472

East Asian (EAS) AF: 0.141 AC: 729 AN: 5164

South Asian (SAS) AF: 0.0691 AC: 333 AN: 4818

European-Finnish (FIN) AF: 0.0523 AC: 554 AN: 10588

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0757 AC: 5145 AN: 67994

Other (OTH) AF: 0.100 AC: 212 AN: 2112

Alfa AF: 0.0779 Hom.: 80

Bravo AF: 0.0906

Asia WGS AF: 0.125 AC: 433 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.51
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs18478; hg19: chr22-35163778;