rs9607195

Variant names:

• chr22-34809849-G-A
• rs9607195
• ENST00000668433.1:n.344-50788C>T

Variant summary

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

The ENST00000668433.1(LINC02885):​n.344-50788C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,130 control chromosomes in the GnomAD database, including 6,612 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 0.27 (6612 hom., cov: 33)
• Consequence: LINC02885 ENST00000668433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02885	NR_138042.1	n.461-49362C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02885	ENST00000668433.1	n.344-50788C>T		intron_variant	Intron 3 of 3
LINC02885	ENST00000801714.1	n.34+32944C>T		intron_variant	Intron 1 of 2
LINC02885	ENST00000801715.1	n.34+32944C>T		intron_variant	Intron 1 of 2
LINC02885	ENST00000801716.1	n.30+32944C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40431 AN: 152010 Hom.: 6602 Cov.: 33

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.266 AC: 40455 AN: 152130 Hom.: 6612 Cov.: 33 AF XY: 0.274 AC XY: 20373 AN XY: 74362

African (AFR) AF: 0.0796 AC: 3307 AN: 41526

American (AMR) AF: 0.319 AC: 4883 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 938 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1259 AN: 5162

South Asian (SAS) AF: 0.463 AC: 2231 AN: 4820

European-Finnish (FIN) AF: 0.425 AC: 4487 AN: 10566

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22282 AN: 67972

Other (OTH) AF: 0.278 AC: 587 AN: 2110

Alfa AF: 0.301 Hom.: 21329

Bravo AF: 0.247

Asia WGS AF: 0.359 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.25
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs9607195; hg19: chr22-35205840;