16-65369318-G-T

Position:

• chr16-65369318-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC00922 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00922	NR_027755.2	n.215-5510C>A		intron_variant
LINC00922	NR_174971.1	n.543+1718C>A		intron_variant
LOC124903780	XR_007065224.1	n.1284-1779G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00922	ENST00000564041.5	n.348+1718C>A		intron_variant		1
LINC00922	ENST00000568492.1	n.20-5510C>A		intron_variant		1
LINC00922	ENST00000569736.5	n.218-5510C>A		intron_variant		1

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

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.0965

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0758

Gnomad4 NFE AF: 0.0782

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0814 Hom.: 334

Bravo AF: 0.147

Asia WGS AF: 0.220 AC: 765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs861749; hg19: chr16-65403221;