rs16921695

Variant names:

• chr8-57145096-T-G
• rs16921695
• ENST00000519241.6:n.166+2211T>G

Variant summary

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

The ENST00000519241.6(LINC01606):​n.166+2211T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,012 control chromosomes in the GnomAD database, including 9,479 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 (9479 hom., cov: 32)
• Consequence: LINC01606 ENST00000519241.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• Publications: 8 publications found

Genes affected

LINC01606 (HGNC:51656): (long intergenic non-protein coding RNA 1606)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01606	ENST00000519241.6	n.166+2211T>G		intron_variant	Intron 1 of 8	3
LINC01606	ENST00000519314.5	n.197+2211T>G		intron_variant	Intron 1 of 3	4
LINC01606	ENST00000655105.1	n.183+2211T>G		intron_variant	Intron 1 of 8

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49002 AN: 151896 Hom.: 9442 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.323 AC: 49091 AN: 152012 Hom.: 9479 Cov.: 32 AF XY: 0.320 AC XY: 23739 AN XY: 74296

African (AFR) AF: 0.550 AC: 22765 AN: 41414

American (AMR) AF: 0.249 AC: 3808 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3470

East Asian (EAS) AF: 0.166 AC: 859 AN: 5170

South Asian (SAS) AF: 0.191 AC: 918 AN: 4810

European-Finnish (FIN) AF: 0.240 AC: 2535 AN: 10576

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.239 AC: 16276 AN: 67976

Other (OTH) AF: 0.323 AC: 681 AN: 2108

Alfa AF: 0.273 Hom.: 8485

Bravo AF: 0.334

Asia WGS AF: 0.214 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.72
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs16921695; hg19: chr8-58057655;