rs16922670

Variant names:

• chr9-103261938-T-C
• rs16922670
• ENST00000411575.5:n.772+2586A>G

Variant summary

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

The ENST00000411575.5(LINC01492):​n.772+2586A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,208 control chromosomes in the GnomAD database, including 2,351 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 0.16 (2351 hom., cov: 32)
• Consequence: LINC01492 ENST00000411575.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 5 publications found

Genes affected

LINC01492 (HGNC:51149): (long intergenic non-protein coding RNA 1492)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411575.5. 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
	LINC01492	NR_121578.1		n.771+2586A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01492	ENST00000411575.5	TSL:1	n.772+2586A>G		intron	N/A
	LINC01492	ENST00000806271.1		n.415+2586A>G		intron	N/A
	LINC01492	ENST00000806272.1		n.550+2586A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25021 AN: 152090 Hom.: 2355 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.164 AC: 25016 AN: 152208 Hom.: 2351 Cov.: 32 AF XY: 0.170 AC XY: 12616 AN XY: 74404

African (AFR) AF: 0.142 AC: 5881 AN: 41536

American (AMR) AF: 0.294 AC: 4489 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3468

East Asian (EAS) AF: 0.332 AC: 1717 AN: 5166

South Asian (SAS) AF: 0.144 AC: 696 AN: 4818

European-Finnish (FIN) AF: 0.164 AC: 1736 AN: 10610

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9440 AN: 68002

Other (OTH) AF: 0.168 AC: 354 AN: 2110

Alfa AF: 0.154 Hom.: 6042

Bravo AF: 0.176

Asia WGS AF: 0.221 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.5
DANN	Benign	0.78
PhyloP100		-0.45

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: rs16922670;

hg19: chr9-106024220;