16-9560199-C-T

Variant names:

• chr16-9560199-C-T
• rs1074042
• ENST00000634367.3:n.262+1122C>T

Variant summary

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

The ENST00000634367.3(LINC02177):​n.262+1122C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,108 control chromosomes in the GnomAD database, including 20,388 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 0.51 (20388 hom., cov: 33)
• Consequence: LINC02177 ENST00000634367.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 4 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC132205950	NR_188388.1	n.283+1122C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02177	ENST00000634367.3	n.262+1122C>T		intron_variant	Intron 2 of 4	5
LINC02177	ENST00000653393.3	n.299+1122C>T		intron_variant	Intron 2 of 5
LINC02177	ENST00000701200.1	n.215+1122C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77625 AN: 151992 Hom.: 20360 Cov.: 33

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.511 AC: 77716 AN: 152108 Hom.: 20388 Cov.: 33 AF XY: 0.506 AC XY: 37631 AN XY: 74340

African (AFR) AF: 0.531 AC: 22012 AN: 41488

American (AMR) AF: 0.607 AC: 9277 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2019 AN: 3470

East Asian (EAS) AF: 0.666 AC: 3449 AN: 5180

South Asian (SAS) AF: 0.477 AC: 2298 AN: 4814

European-Finnish (FIN) AF: 0.337 AC: 3553 AN: 10558

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33334 AN: 67994

Other (OTH) AF: 0.527 AC: 1111 AN: 2110

Alfa AF: 0.508 Hom.: 65995

Bravo AF: 0.538

Asia WGS AF: 0.626 AC: 2175 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.42
DANN	Benign	0.78
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1074042; hg19: chr16-9654056;