chr16-76927950-G-A

Variant names:

• chr16-76927950-G-A
• rs3736338
• ENST00000567777.2:n.516G>A

Variant summary

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

The ENST00000567777.2(LINC02125):​n.516G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,984 control chromosomes in the GnomAD database, including 10,921 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 0.35 (10921 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: LINC02125 ENST00000567777.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• Publications: 4 publications found

Genes affected

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

LOC100128497 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100128497		n.76927950G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02125	ENST00000567777.2	n.516G>A		non_coding_transcript_exon_variant	Exon 5 of 5	3
LINC02125	ENST00000751836.1	n.610G>A		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53832 AN: 151860 Hom.: 10905 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.372

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.354 AC: 53876 AN: 151978 Hom.: 10921 Cov.: 32 AF XY: 0.350 AC XY: 26027 AN XY: 74294

African (AFR) AF: 0.166 AC: 6879 AN: 41478

American (AMR) AF: 0.307 AC: 4691 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3470

East Asian (EAS) AF: 0.309 AC: 1592 AN: 5160

South Asian (SAS) AF: 0.308 AC: 1482 AN: 4816

European-Finnish (FIN) AF: 0.440 AC: 4643 AN: 10558

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31424 AN: 67916

Other (OTH) AF: 0.378 AC: 799 AN: 2112

Alfa AF: 0.406 Hom.: 7746

Bravo AF: 0.336

Asia WGS AF: 0.322 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs3736338; hg19: chr16-76961847;