7-17521959-A-G

Variant names:

• chr7-17521959-A-G
• rs10499504
• ENST00000451792.1:n.158+36793T>C

Variant summary

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

The ENST00000451792.1(LINC02889):​n.158+36793T>C 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 151,938 control chromosomes in the GnomAD database, including 1,928 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 (1928 hom., cov: 32)
• Consequence: LINC02889 ENST00000451792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 14 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=-0.83).
• 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.158+36793T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02889	ENST00000451792.1	n.158+36793T>C		intron_variant	Intron 1 of 3	3
LINC02889	ENST00000454003.2	n.52+2138T>C		intron_variant	Intron 1 of 8	3
LINC02889	ENST00000636929.1	n.79+2138T>C		intron_variant	Intron 1 of 10	5

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21372 AN: 151820 Hom.: 1931 Cov.: 32

Gnomad AFR AF: 0.0332

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.141 AC: 21367 AN: 151938 Hom.: 1928 Cov.: 32 AF XY: 0.146 AC XY: 10810 AN XY: 74260

African (AFR) AF: 0.0331 AC: 1377 AN: 41540

American (AMR) AF: 0.207 AC: 3155 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 612 AN: 3460

East Asian (EAS) AF: 0.107 AC: 554 AN: 5170

South Asian (SAS) AF: 0.226 AC: 1090 AN: 4816

European-Finnish (FIN) AF: 0.207 AC: 2181 AN: 10546

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

European-Non Finnish (NFE) AF: 0.176 AC: 11929 AN: 67844

Other (OTH) AF: 0.144 AC: 303 AN: 2106

Alfa AF: 0.164 Hom.: 8273

Bravo AF: 0.134

Asia WGS AF: 0.154 AC: 532 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.81
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10499504; hg19: chr7-17561583;