17-43359227-A-T

Position:

• chr17-43359227-A-T

Variant summary

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

The ENST00000658096.1(LINC00910):​n.696-2697T>A 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 0.508 in 152,118 control chromosomes in the GnomAD database, including 23,672 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 0.51 (23672 hom., cov: 37)
• Consequence: LINC00910 ENST00000658096.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00910	ENST00000658096.1	n.696-2697T>A		intron_variant, non_coding_transcript_variant
LINC00910	ENST00000661340.1	n.709-9898T>A		intron_variant, non_coding_transcript_variant
LINC00910	ENST00000662750.1	n.709-17768T>A		intron_variant, non_coding_transcript_variant
LINC00910	ENST00000664824.1	n.696-17768T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77241 AN: 152000 Hom.: 23612 Cov.: 37

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.508 AC: 77350 AN: 152118 Hom.: 23672 Cov.: 37 AF XY: 0.510 AC XY: 37934 AN XY: 74366

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.483

Alfa AF: 0.254 Hom.: 579

Bravo AF: 0.520

Asia WGS AF: 0.504 AC: 1754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4793237; hg19: chr17-41436595;