rs1979096

Variant names:

• chr7-17521125-T-A
• rs1979096
• ENST00000451792.1:n.159-37591A>T

Your query was ambiguous. Multiple possible variants found:

• chr7-17521125-T-A
• chr7-17521125-T-C

Variant summary

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

The ENST00000451792.1(LINC02889):​n.159-37591A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,204 control chromosomes in the GnomAD database, including 1,931 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 0.14 (1931 hom., cov: 33)
• Consequence: LINC02889 ENST00000451792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 5 publications found

Genes affected

LINC02889 (HGNC:55071): (long intergenic non-protein coding RNA 2889)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02889	NR_110013.1	n.159-37591A>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02889	ENST00000451792.1	n.159-37591A>T		intron_variant	Intron 1 of 3	3
LINC02889	ENST00000454003.2	n.52+2972A>T		intron_variant	Intron 1 of 8	3
LINC02889	ENST00000636929.1	n.79+2972A>T		intron_variant	Intron 1 of 10	5

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21428 AN: 152086 Hom.: 1934 Cov.: 33

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.141 AC: 21423 AN: 152204 Hom.: 1931 Cov.: 33 AF XY: 0.146 AC XY: 10853 AN XY: 74428

African (AFR) AF: 0.0334 AC: 1388 AN: 41570

American (AMR) AF: 0.207 AC: 3164 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3468

East Asian (EAS) AF: 0.108 AC: 558 AN: 5184

South Asian (SAS) AF: 0.226 AC: 1091 AN: 4822

European-Finnish (FIN) AF: 0.207 AC: 2192 AN: 10592

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11946 AN: 67954

Other (OTH) AF: 0.145 AC: 307 AN: 2114

Alfa AF: 0.0850 Hom.: 126

Bravo AF: 0.134

Asia WGS AF: 0.155 AC: 537 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1979096; hg19: chr7-17560749;