rs1468769

Variant names:

• chr16-9569798-C-T
• rs1468769
• ENST00000634367.3:n.622+3208C>T

Variant summary

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

The ENST00000634367.3(LINC02177):​n.622+3208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,928 control chromosomes in the GnomAD database, including 12,159 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 0.39 (12159 hom., cov: 32)
• Consequence: LINC02177 ENST00000634367.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 1 publications found

Genes affected

LINC02177 (HGNC:53039): (long intergenic non-protein coding RNA 2177)

LOC132205950 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC132205950	NR_188388.1	n.643+3208C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02177	ENST00000634367.3	n.622+3208C>T		intron_variant	Intron 4 of 4	5
LINC02177	ENST00000653393.3	n.659+3208C>T		intron_variant	Intron 4 of 5
LINC02177	ENST00000701200.1	n.575+3208C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59631 AN: 151810 Hom.: 12153 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.393 AC: 59655 AN: 151928 Hom.: 12159 Cov.: 32 AF XY: 0.392 AC XY: 29111 AN XY: 74248

African (AFR) AF: 0.278 AC: 11495 AN: 41420

American (AMR) AF: 0.491 AC: 7500 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1648 AN: 3468

East Asian (EAS) AF: 0.359 AC: 1856 AN: 5168

South Asian (SAS) AF: 0.393 AC: 1897 AN: 4822

European-Finnish (FIN) AF: 0.376 AC: 3961 AN: 10546

Middle Eastern (MID) AF: 0.472 AC: 137 AN: 290

European-Non Finnish (NFE) AF: 0.440 AC: 29870 AN: 67928

Other (OTH) AF: 0.407 AC: 860 AN: 2112

Alfa AF: 0.425 Hom.: 11533

Bravo AF: 0.392

Asia WGS AF: 0.408 AC: 1420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	6.8
DANN	Benign	0.76
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1468769; hg19: chr16-9663655;