16-85935285-T-G

Variant names:

• chr16-85935285-T-G
• rs450443
• ENST00000598933.3:n.797A>C

Variant summary

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

The ENST00000598933.3(LINC02132):​n.797A>C 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 0.35 in 151,982 control chromosomes in the GnomAD database, including 10,498 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 (10498 hom., cov: 32)
  • Exomes 𝑓: 0.21 (0 hom.)
• Consequence: LINC02132 ENST00000598933.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 4 publications found

Genes affected

LINC02132 (HGNC:52992): (long intergenic non-protein coding RNA 2132)

ENSG00000285163 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000598933.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02132	ENST00000598933.3	TSL:2	n.797A>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000285163	ENST00000645383.1		n.393+3011T>G		intron	N/A
	ENSG00000285163	ENST00000646214.1		n.78-10131T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53166 AN: 151848 Hom.: 10466 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.302

GnomAD4 exome AF: 0.214 AC: 3 AN: 14 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) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AF: 0.333 AC: 2 AN: 6

GnomAD4 genome AF: 0.350 AC: 53251 AN: 151968 Hom.: 10498 Cov.: 32 AF XY: 0.353 AC XY: 26207 AN XY: 74292

African (AFR) AF: 0.540 AC: 22343 AN: 41406

American (AMR) AF: 0.275 AC: 4196 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3460

East Asian (EAS) AF: 0.325 AC: 1681 AN: 5168

South Asian (SAS) AF: 0.302 AC: 1453 AN: 4814

European-Finnish (FIN) AF: 0.345 AC: 3642 AN: 10562

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.267 AC: 18140 AN: 67978

Other (OTH) AF: 0.299 AC: 631 AN: 2108

Alfa AF: 0.333 Hom.: 1204

Bravo AF: 0.357

Asia WGS AF: 0.327 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.20
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs450443; hg19: chr16-85968891;