rs11651341

Variant names:

• chr17-43350693-T-C
• rs11651341
• ENST00000658096.1:n.834+5699A>G

Variant summary

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

The ENST00000658096.1(LINC00910):​n.834+5699A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,032 control chromosomes in the GnomAD database, including 8,103 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 0.32 (8103 hom., cov: 32)
• Consequence: LINC00910 ENST00000658096.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.478 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.834+5699A>G		intron_variant	Intron 5 of 6
LINC00910	ENST00000661340.1	n.709-1364A>G		intron_variant	Intron 4 of 4
LINC00910	ENST00000662750.1	n.709-9234A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48556 AN: 151914 Hom.: 8097 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.320 AC: 48587 AN: 152032 Hom.: 8103 Cov.: 32 AF XY: 0.326 AC XY: 24234 AN XY: 74326

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.339

Alfa AF: 0.335 Hom.: 11606

Bravo AF: 0.305

Asia WGS AF: 0.416 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11651341; hg19: chr17-41428061;