16-65369318-G-T

Variant names:

• chr16-65369318-G-T
• rs861749
• ENST00000564041.5:n.348+1718C>A

Variant summary

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

The ENST00000564041.5(LINC00922):​n.348+1718C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 151,990 control chromosomes in the GnomAD database, including 1,833 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 0.14 (1833 hom., cov: 32)
• Consequence: LINC00922 ENST00000564041.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568
• Publications: 3 publications found

Genes affected

LINC00922 (HGNC:27545): (long intergenic non-protein coding RNA 922)

ENSG00000260364 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564041.5. 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
	LINC00922	NR_027755.2		n.215-5510C>A		intron	N/A
	LINC00922	NR_174971.1		n.543+1718C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00922	ENST00000564041.5	TSL:1	n.348+1718C>A		intron	N/A
	LINC00922	ENST00000568492.1	TSL:1	n.20-5510C>A		intron	N/A
	LINC00922	ENST00000569736.5	TSL:1	n.218-5510C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20718 AN: 151870 Hom.: 1830 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.136 AC: 20739 AN: 151990 Hom.: 1833 Cov.: 32 AF XY: 0.140 AC XY: 10423 AN XY: 74274

African (AFR) AF: 0.215 AC: 8889 AN: 41430

American (AMR) AF: 0.172 AC: 2624 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 335 AN: 3470

East Asian (EAS) AF: 0.329 AC: 1690 AN: 5134

South Asian (SAS) AF: 0.148 AC: 716 AN: 4826

European-Finnish (FIN) AF: 0.0758 AC: 801 AN: 10572

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0782 AC: 5313 AN: 67974

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.0822 Hom.: 369

Bravo AF: 0.147

Asia WGS AF: 0.220 AC: 765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.56
DANN	Benign	0.46
PhyloP100		-0.57

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: rs861749;

hg19: chr16-65403221;