16-65502717-C-T

Variant names:

• chr16-65502717-C-T
• rs1423828
• ENST00000564041.5:n.19+69054G>A

Variant summary

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

The ENST00000564041.5(LINC00922):​n.19+69054G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,032 control chromosomes in the GnomAD database, including 8,362 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 (8362 hom., cov: 32)
• Consequence: LINC00922 ENST00000564041.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00922	NR_027755.2	n.214+69054G>A		intron_variant	Intron 2 of 8
LINC00922	NR_174971.1	n.214+69054G>A		intron_variant	Intron 2 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00922	ENST00000564041.5	n.19+69054G>A		intron_variant	Intron 1 of 9	1
LINC00922	ENST00000568492.1	n.19+69054G>A		intron_variant	Intron 1 of 5	1
LINC00922	ENST00000569736.5	n.217+69054G>A		intron_variant	Intron 2 of 8	1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48326 AN: 151914 Hom.: 8360 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.318 AC: 48346 AN: 152032 Hom.: 8362 Cov.: 32 AF XY: 0.312 AC XY: 23223 AN XY: 74324

African (AFR) AF: 0.208 AC: 8644 AN: 41458

American (AMR) AF: 0.275 AC: 4201 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1039 AN: 3470

East Asian (EAS) AF: 0.110 AC: 570 AN: 5172

South Asian (SAS) AF: 0.383 AC: 1843 AN: 4812

European-Finnish (FIN) AF: 0.313 AC: 3305 AN: 10572

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27501 AN: 67960

Other (OTH) AF: 0.329 AC: 694 AN: 2108

Alfa AF: 0.377 Hom.: 21953

Bravo AF: 0.305

Asia WGS AF: 0.272 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.37
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs1423828; hg19: chr16-65536620;