9-92142335-G-A

Variant names:

• chr9-92142335-G-A
• rs3858095
• ENST00000808771.1:n.630G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000808771.1(ENSG00000290644):​n.630G>A 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 0.452 in 152,078 control chromosomes in the GnomAD database, including 18,845 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 0.45 (18845 hom., cov: 32)
• Consequence: ENSG00000290644 ENST00000808771.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370
• Publications: 6 publications found

Genes affected

ENSG00000290644 (HGNC:):

LINC00475 (HGNC:23569): (long intergenic non-protein coding RNA 475)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808771.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00475	NR_027341.1		n.184+685G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290644	ENST00000808771.1		n.630G>A		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000290644	ENST00000367276.9	TSL:2	n.353+685G>A		intron	N/A
	ENSG00000290644	ENST00000416438.6	TSL:2	n.184+685G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68640 AN: 151960 Hom.: 18799 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.452 AC: 68740 AN: 152078 Hom.: 18845 Cov.: 32 AF XY: 0.456 AC XY: 33929 AN XY: 74356

African (AFR) AF: 0.766 AC: 31772 AN: 41504

American (AMR) AF: 0.490 AC: 7486 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3468

East Asian (EAS) AF: 0.425 AC: 2190 AN: 5152

South Asian (SAS) AF: 0.455 AC: 2194 AN: 4824

European-Finnish (FIN) AF: 0.307 AC: 3249 AN: 10576

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19529 AN: 67952

Other (OTH) AF: 0.395 AC: 833 AN: 2110

Alfa AF: 0.361 Hom.: 6581

Bravo AF: 0.477

Asia WGS AF: 0.472 AC: 1642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	17
DANN	Benign	0.95
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs3858095; hg19: chr9-94904617; COSMIC: COSV66153921;