rs4534897

Positions:

• chr17-43354440-A-G

Variant summary

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

The ENST00000658096.1(LINC00910):​n.834+1952T>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 0.32 in 152,088 control chromosomes in the GnomAD database, including 8,129 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 (8129 hom., cov: 32)
• Consequence: LINC00910 ENST00000658096.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

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=-0.9).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00910	ENST00000658096.1	n.834+1952T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48638 AN: 151970 Hom.: 8123 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.405

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: 48668 AN: 152088 Hom.: 8129 Cov.: 32 AF XY: 0.326 AC XY: 24263 AN XY: 74330

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.339

Alfa AF: 0.340 Hom.: 4281

Bravo AF: 0.306

Asia WGS AF: 0.416 AC: 1446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4534897; hg19: chr17-41431808;