rs2097365

Variant names:

• chr22-34936923-G-A
• rs2097365
• ENST00000668433.1:n.203-34160C>T

Variant summary

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

The ENST00000668433.1(LINC02885):​n.203-34160C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0405 in 152,150 control chromosomes in the GnomAD database, including 170 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 0.041 (170 hom., cov: 32)
• Consequence: LINC02885 ENST00000668433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968
• Publications: 1 publications found

Genes affected

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02885	NR_138042.1	n.199-34160C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02885	ENST00000668433.1	n.203-34160C>T		intron_variant	Intron 2 of 3
LINC02885	ENST00000700833.2	n.96-34160C>T		intron_variant	Intron 1 of 3
LINC02885	ENST00000754702.1	n.366-38967C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0405 AC: 6155 AN: 152032 Hom.: 169 Cov.: 32

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0362

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.00809

Gnomad SAS AF: 0.0444

Gnomad FIN AF: 0.0623

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0568

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0405 AC: 6163 AN: 152150 Hom.: 170 Cov.: 32 AF XY: 0.0405 AC XY: 3010 AN XY: 74366

African (AFR) AF: 0.0130 AC: 539 AN: 41514

American (AMR) AF: 0.0362 AC: 553 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0531 AC: 184 AN: 3468

East Asian (EAS) AF: 0.00811 AC: 42 AN: 5180

South Asian (SAS) AF: 0.0447 AC: 215 AN: 4812

European-Finnish (FIN) AF: 0.0623 AC: 659 AN: 10574

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0568 AC: 3864 AN: 68000

Other (OTH) AF: 0.0451 AC: 95 AN: 2108

Alfa AF: 0.0443 Hom.: 19

Bravo AF: 0.0376

Asia WGS AF: 0.0330 AC: 114 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.47
DANN	Benign	0.12
PhyloP100		-0.97
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2097365; hg19: chr22-35332912;