rs3815784

Variant names:

• chr16-52083741-G-A
• rs3815784
• ENST00000561513.6:n.1045C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-52083741-G-A
• chr16-52083741-G-C
• chr16-52083741-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000561513.6(LINC00919):​n.1045C>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 0.00138 in 157,160 control chromosomes in the GnomAD database, including 3 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 0.0014 (3 hom., cov: 32)
  • Exomes 𝑓: 0.00060 (0 hom.)
• Consequence: LINC00919 ENST00000561513.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 1 publications found

Genes affected

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

LINC02180 (HGNC:53042): (long intergenic non-protein coding RNA 2180)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00141 (214/152126) while in subpopulation EAS AF = 0.0341 (176/5164). AF 95% confidence interval is 0.03. There are 3 homozygotes in GnomAd4. There are 116 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00919	NR_038233.1	n.982C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00919	ENST00000561513.6	n.1045C>T		non_coding_transcript_exon_variant	Exon 3 of 3	2
LINC00919	ENST00000565742.1	n.870C>T		non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC00919	ENST00000655537.2	n.937C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.00140 AC: 213 AN: 152008 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.000507

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000657

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.0338

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00144

GnomAD4 exome AF: 0.000596 AC: 3 AN: 5034 Hom.: 0 Cov.: 0 AF XY: 0.000366 AC XY: 1 AN XY: 2732

African (AFR) AF: 0.00 AC: 0 AN: 12

American (AMR) AF: 0.00 AC: 0 AN: 1010

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22

East Asian (EAS) AF: 0.0149 AC: 3 AN: 202

South Asian (SAS) AF: 0.00 AC: 0 AN: 520

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 54

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 3032

Other (OTH) AF: 0.00 AC: 0 AN: 178

GnomAD4 genome AF: 0.00141 AC: 214 AN: 152126 Hom.: 3 Cov.: 32 AF XY: 0.00156 AC XY: 116 AN XY: 74374

African (AFR) AF: 0.000506 AC: 21 AN: 41526

American (AMR) AF: 0.0000656 AC: 1 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3468

East Asian (EAS) AF: 0.0341 AC: 176 AN: 5164

South Asian (SAS) AF: 0.000621 AC: 3 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 67968

Other (OTH) AF: 0.00142 AC: 3 AN: 2112

Alfa AF: 0.000459 Hom.: 1

Bravo AF: 0.00206

Asia WGS AF: 0.00953 AC: 33 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.47
PhyloP100		0.087

Splicing

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

Other links and lift over

dbSNP: rs3815784; hg19: chr16-52117653;