16-52073899-T-A

Variant names:

• chr16-52073899-T-A
• rs17201113
• ENST00000622950.3:n.4A>T

Variant summary

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

The ENST00000622950.3(LINC00919):​n.4A>T 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 0.0193 in 459,272 control chromosomes in the GnomAD database, including 133 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 0.017 (35 hom., cov: 33)
  • Exomes 𝑓: 0.020 (98 hom.)
• Consequence: LINC00919 ENST00000622950.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.49
• Publications: 4 publications found

Genes affected

LINC00919 (HGNC:48610): (long intergenic non-protein coding RNA 919)

LINC02911 (HGNC:44658): (long intergenic non-protein coding RNA 2911)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0623 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000622950.3. 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
	LINC00919	ENST00000622950.3	TSL:2	n.4A>T		non_coding_transcript_exon	Exon 1 of 6
	LINC00919	ENST00000816931.1		n.286A>T		non_coding_transcript_exon	Exon 3 of 5
	LINC00919	ENST00000566314.6	TSL:3	n.286+994A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0173 AC: 2626 AN: 152142 Hom.: 35 Cov.: 33

Gnomad AFR AF: 0.00425

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0397

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0112

Gnomad FIN AF: 0.00443

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0256

Gnomad OTH AF: 0.0263

GnomAD2 exomes AF: 0.0192 AC: 2449 AN: 127442 AF XY: 0.0193

Gnomad AFR exome AF: 0.00214

Gnomad AMR exome AF: 0.0224

Gnomad ASJ exome AF: 0.0264

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00433

Gnomad NFE exome AF: 0.0269

Gnomad OTH exome AF: 0.0366

GnomAD4 exome AF: 0.0203 AC: 6239 AN: 307012 Hom.: 98 Cov.: 1 AF XY: 0.0202 AC XY: 3532 AN XY: 174584

African (AFR) AF: 0.00564 AC: 49 AN: 8684

American (AMR) AF: 0.0226 AC: 616 AN: 27198

Ashkenazi Jewish (ASJ) AF: 0.0261 AC: 282 AN: 10792

East Asian (EAS) AF: 0.00 AC: 0 AN: 9220

South Asian (SAS) AF: 0.0110 AC: 654 AN: 59670

European-Finnish (FIN) AF: 0.00486 AC: 60 AN: 12346

Middle Eastern (MID) AF: 0.0703 AC: 195 AN: 2772

European-Non Finnish (NFE) AF: 0.0246 AC: 3993 AN: 162022

Other (OTH) AF: 0.0273 AC: 390 AN: 14308

GnomAD4 genome AF: 0.0172 AC: 2622 AN: 152260 Hom.: 35 Cov.: 33 AF XY: 0.0162 AC XY: 1209 AN XY: 74446

African (AFR) AF: 0.00424 AC: 176 AN: 41556

American (AMR) AF: 0.0243 AC: 372 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0397 AC: 138 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.0114 AC: 55 AN: 4822

European-Finnish (FIN) AF: 0.00443 AC: 47 AN: 10618

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0255 AC: 1737 AN: 68012

Other (OTH) AF: 0.0255 AC: 54 AN: 2114

Alfa AF: 0.0213 Hom.: 5

Bravo AF: 0.0185

Asia WGS AF: 0.00491 AC: 17 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0060
DANN	Benign	0.55
PhyloP100		-3.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17201113; hg19: chr16-52107811;