rs4083242

Variant names:

• chr16-86334920-G-A
• rs4083242
• ENST00000594203.5:n.1538-1013C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-86334920-G-A
• chr16-86334920-G-C

Variant summary

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

The ENST00000664042.1(LINC00917):​n.506C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,010 control chromosomes in the GnomAD database, including 11,674 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 0.35 (11674 hom., cov: 32)
• Consequence: LINC00917 ENST00000664042.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 5 publications found

Genes affected

LINC00917 (HGNC:48607): (long intergenic non-protein coding RNA 917)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664042.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00917	NR_024406.1		n.1484-1013C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00917	ENST00000594203.5	TSL:1	n.1538-1013C>T		intron	N/A
	LINC00917	ENST00000600892.5	TSL:1	n.391+758C>T		intron	N/A
	LINC00917	ENST00000664042.1		n.506C>T		non_coding_transcript_exon	Exon 4 of 6

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53729 AN: 151892 Hom.: 11674 Cov.: 32

Gnomad AFR AF: 0.0863

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.353 AC: 53735 AN: 152010 Hom.: 11674 Cov.: 32 AF XY: 0.360 AC XY: 26746 AN XY: 74278

African (AFR) AF: 0.0863 AC: 3581 AN: 41514

American (AMR) AF: 0.406 AC: 6207 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1657 AN: 3472

East Asian (EAS) AF: 0.548 AC: 2823 AN: 5152

South Asian (SAS) AF: 0.367 AC: 1766 AN: 4806

European-Finnish (FIN) AF: 0.548 AC: 5780 AN: 10544

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30494 AN: 67946

Other (OTH) AF: 0.378 AC: 795 AN: 2102

Alfa AF: 0.338 Hom.: 6640

Bravo AF: 0.332

Asia WGS AF: 0.395 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.044
DANN	Benign	0.59
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4083242;

hg19: chr16-86368526;