17-43354440-A-G

Variant names:

• chr17-43354440-A-G
• rs4534897
• ENST00000658096.1:n.834+1952T>C

Variant summary

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

The ENST00000658096.1(LINC00910):​n.834+1952T>C 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 152,088 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658096.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00910	ENST00000658096.1		n.834+1952T>C		intron	N/A
	LINC00910	ENST00000661340.1		n.709-5111T>C		intron	N/A
	LINC00910	ENST00000662750.1		n.709-12981T>C		intron	N/A

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

African (AFR) AF: 0.238 AC: 9879 AN: 41498

American (AMR) AF: 0.332 AC: 5068 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1250 AN: 3472

East Asian (EAS) AF: 0.369 AC: 1906 AN: 5168

South Asian (SAS) AF: 0.495 AC: 2383 AN: 4818

European-Finnish (FIN) AF: 0.405 AC: 4277 AN: 10560

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22826 AN: 67986

Other (OTH) AF: 0.339 AC: 714 AN: 2108

Alfa AF: 0.338 Hom.: 5710

Bravo AF: 0.306

Asia WGS AF: 0.416 AC: 1446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.38
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4534897; hg19: chr17-41431808;