rs11657004

chr17-43365383-A-G

Variant summary

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

The ENST00000658096.1(LINC00910):n.696-8853T>C 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 0.427 in 151,996 control chromosomes in the GnomAD database, including 14,941 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 0.43 (14941 hom., cov: 32)
• Consequence: LINC00910 ENST00000658096.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.61

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.596 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.696-8853T>C		intron_variant, non_coding_transcript_variant
LINC00910	ENST00000661340.1	n.708+12288T>C		intron_variant, non_coding_transcript_variant
LINC00910	ENST00000662750.1	n.708+12288T>C		intron_variant, non_coding_transcript_variant
LINC00910	ENST00000664824.1	n.695+12288T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64857 AN: 151878 Hom.: 14896 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.427 AC: 64947 AN: 151996 Hom.: 14941 Cov.: 32 AF XY: 0.431 AC XY: 32020 AN XY: 74304

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.419

Alfa AF: 0.370 Hom.: 5135

Bravo AF: 0.427

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.51
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11657004; hg19: chr17-41442751;