7-17526629-T-C

Position:

• chr7-17526629-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110013.1(LINC02889):​n.158+32123A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,822 control chromosomes in the GnomAD database, including 28,035 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 0.61 (28035 hom., cov: 31)
• Consequence: LINC02889 NR_110013.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02889	NR_110013.1	n.158+32123A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02889	ENST00000451792.1	n.158+32123A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91875 AN: 151704 Hom.: 28016 Cov.: 31

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.606 AC: 91945 AN: 151822 Hom.: 28035 Cov.: 31 AF XY: 0.604 AC XY: 44855 AN XY: 74216

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.618

Alfa AF: 0.582 Hom.: 3304

Bravo AF: 0.613

Asia WGS AF: 0.614 AC: 2135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1375237; hg19: chr7-17566253;