17-43346885-G-A

Variant names:

• chr17-43346885-G-A
• rs9646417
• ENST00000658096.1:n.835-5426C>T

Variant summary

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

The ENST00000658096.1(LINC00910):​n.835-5426C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,934 control chromosomes in the GnomAD database, including 7,510 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 0.30 (7510 hom., cov: 31)
• Consequence: LINC00910 ENST00000658096.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 9 publications found

Genes affected

LINC00910 (HGNC:44361): (long intergenic non-protein coding RNA 910)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00910	ENST00000658096.1	n.835-5426C>T		intron_variant	Intron 5 of 6
LINC00910	ENST00000662750.1	n.709-5426C>T		intron_variant	Intron 4 of 4
LINC00910	ENST00000663186.1	n.141-5426C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45917 AN: 151816 Hom.: 7511 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.302 AC: 45912 AN: 151934 Hom.: 7510 Cov.: 31 AF XY: 0.309 AC XY: 22926 AN XY: 74228

African (AFR) AF: 0.179 AC: 7407 AN: 41448

American (AMR) AF: 0.322 AC: 4925 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1218 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1909 AN: 5166

South Asian (SAS) AF: 0.494 AC: 2379 AN: 4820

European-Finnish (FIN) AF: 0.405 AC: 4250 AN: 10500

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22775 AN: 67942

Other (OTH) AF: 0.327 AC: 689 AN: 2110

Alfa AF: 0.317 Hom.: 4136

Bravo AF: 0.285

Asia WGS AF: 0.405 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.94
DANN	Benign	0.57
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs9646417; hg19: chr17-41424253;