16-76584018-T-C

Variant names:

• chr16-76584018-T-C
• rs7500366
• ENST00000655556.1:n.3733+30111T>C

Variant summary

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

The ENST00000655556.1(ENSG00000287694):​n.3733+30111T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,112 control chromosomes in the GnomAD database, including 20,396 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 (20396 hom., cov: 33)
• Consequence: ENSG00000287694 ENST00000655556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148
• Publications: 1 publications found

Genes affected

ENSG00000287694 (HGNC:):

LINC02125 (HGNC:52982): (long intergenic non-protein coding RNA 2125)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 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
ENSG00000287694	ENST00000655556.1	n.3733+30111T>C		intron_variant	Intron 23 of 24			ENSP00000499374.1
ENSG00000287694	ENST00000563764.2	n.157+30111T>C		intron_variant	Intron 2 of 3	3		ENSP00000455258.1
LINC02125	ENST00000751919.1	n.133+4202T>C		intron_variant	Intron 2 of 3
LINC02125	ENST00000751920.1	n.286+4202T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77581 AN: 151994 Hom.: 20404 Cov.: 33

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.510 AC: 77584 AN: 152112 Hom.: 20396 Cov.: 33 AF XY: 0.513 AC XY: 38187 AN XY: 74368

African (AFR) AF: 0.379 AC: 15737 AN: 41504

American (AMR) AF: 0.530 AC: 8102 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1976 AN: 3470

East Asian (EAS) AF: 0.601 AC: 3102 AN: 5158

South Asian (SAS) AF: 0.540 AC: 2605 AN: 4820

European-Finnish (FIN) AF: 0.599 AC: 6339 AN: 10580

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37867 AN: 67988

Other (OTH) AF: 0.506 AC: 1068 AN: 2112

Alfa AF: 0.541 Hom.: 10498

Bravo AF: 0.499

Asia WGS AF: 0.527 AC: 1833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.72
PhyloP100		0.15

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7500366; hg19: chr16-76617915;