17-43359227-A-T

Variant names:

• chr17-43359227-A-T
• rs4793237
• ENST00000658096.1:n.696-2697T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658096.1(LINC00910):​n.696-2697T>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00910	ENST00000658096.1	n.696-2697T>A		intron_variant	Intron 4 of 6
LINC00910	ENST00000661340.1	n.709-9898T>A		intron_variant	Intron 4 of 4
LINC00910	ENST00000662750.1	n.709-17768T>A		intron_variant	Intron 4 of 4

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

African (AFR) AF: 0.869 AC: 36114 AN: 41568

American (AMR) AF: 0.419 AC: 6386 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1260 AN: 3466

East Asian (EAS) AF: 0.397 AC: 2056 AN: 5174

South Asian (SAS) AF: 0.541 AC: 2609 AN: 4826

European-Finnish (FIN) AF: 0.408 AC: 4308 AN: 10560

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23201 AN: 67952

Other (OTH) AF: 0.483 AC: 1021 AN: 2114

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
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs4793237; hg19: chr17-41436595;