rs4795885

Variant names:

• chr17-34176523-G-A
• rs4795885
• ENST00000566930.6:n.730-1800C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-34176523-G-A
• chr17-34176523-G-C

Variant summary

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

The ENST00000566930.6(LINC01989):​n.730-1800C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,156 control chromosomes in the GnomAD database, including 58,674 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 0.88 (58669 hom., cov: 31)
  • Exomes 𝑓: 0.79 (5 hom.)
• Consequence: LINC01989 ENST00000566930.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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.730-1800C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01989	ENST00000566930.6	TSL:1	n.730-1800C>T		intron	N/A
	LINC01989	ENST00000580792.2	TSL:3	n.393-6964C>T		intron	N/A
	LINC01989	ENST00000584724.5	TSL:3	n.85+6238C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133088 AN: 152024 Hom.: 58603 Cov.: 31

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.860

GnomAD4 exome AF: 0.786 AC: 11 AN: 14 Hom.: 5 Cov.: 0 AF XY: 0.750 AC XY: 9 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.800 AC: 8 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.876 AC: 133213 AN: 152142 Hom.: 58669 Cov.: 31 AF XY: 0.878 AC XY: 65253 AN XY: 74332

African (AFR) AF: 0.969 AC: 40227 AN: 41512

American (AMR) AF: 0.873 AC: 13344 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2975 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5159 AN: 5162

South Asian (SAS) AF: 0.963 AC: 4640 AN: 4818

European-Finnish (FIN) AF: 0.836 AC: 8843 AN: 10582

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55122 AN: 67990

Other (OTH) AF: 0.861 AC: 1815 AN: 2108

Alfa AF: 0.857 Hom.: 8109

Bravo AF: 0.881

Asia WGS AF: 0.978 AC: 3403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.19
DANN	Benign	0.49
PhyloP100		-0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4795885;

hg19: chr17-32503542;