rs9646417

chr17-43346885-G-Achr17-43346885-G-T

Variant summary

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

The ENST00000658096.1(LINC00910):n.835-5426C>T 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 0.302 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00910	ENST00000658096.1	n.835-5426C>T		intron_variant, non_coding_transcript_variant
LINC00910	ENST00000662750.1	n.709-5426C>T		intron_variant, non_coding_transcript_variant
LINC00910	ENST00000663186.1	n.141-5426C>T		intron_variant, non_coding_transcript_variant
LINC00910	ENST00000664824.1	n.696-5426C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.327

Alfa AF: 0.315 Hom.: 3699

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9646417; hg19: chr17-41424253;