17-34176349-A-G

Variant names:

• chr17-34176349-A-G
• rs4795884
• ENST00000566930.6:n.730-1626T>C

Variant summary

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

The ENST00000566930.6(LINC01989):​n.730-1626T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,114 control chromosomes in the GnomAD database, including 32,387 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 0.63 (32387 hom., cov: 32)
• Consequence: LINC01989 ENST00000566930.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.896
• Publications: 3 publications found

Genes affected

LINC01989 (HGNC:52821): (long intergenic non-protein coding RNA 1989)

ENSG00000264990 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000566930.6. 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
	LINC01989	NR_110748.1		n.730-1626T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01989	ENST00000566930.6	TSL:1	n.730-1626T>C		intron	N/A
	LINC01989	ENST00000580792.2	TSL:3	n.393-6790T>C		intron	N/A
	LINC01989	ENST00000584724.5	TSL:3	n.85+6412T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95489 AN: 151996 Hom.: 32321 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.629 AC: 95612 AN: 152114 Hom.: 32387 Cov.: 32 AF XY: 0.632 AC XY: 46987 AN XY: 74356

African (AFR) AF: 0.889 AC: 36894 AN: 41518

American (AMR) AF: 0.626 AC: 9579 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1913 AN: 3466

East Asian (EAS) AF: 0.766 AC: 3955 AN: 5166

South Asian (SAS) AF: 0.566 AC: 2725 AN: 4814

European-Finnish (FIN) AF: 0.542 AC: 5735 AN: 10574

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33007 AN: 67970

Other (OTH) AF: 0.599 AC: 1265 AN: 2112

Alfa AF: 0.567 Hom.: 13491

Bravo AF: 0.646

Asia WGS AF: 0.675 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.69
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs4795884; hg19: chr17-32503368;