16-52607274-T-C

Variant names:

• chr16-52607274-T-C
• rs3104793
• ENST00000564361.2:n.208T>C

Variant summary

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

The ENST00000564361.2(LINC03064):​n.208T>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 0.495 in 152,416 control chromosomes in the GnomAD database, including 19,498 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 0.50 (19465 hom., cov: 33)
  • Exomes 𝑓: 0.44 (33 hom.)
• Consequence: LINC03064 ENST00000564361.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 17 publications found

Genes affected

LINC03064 (HGNC:56372): (long intergenic non-protein coding RNA 3064)

CASC16 (HGNC:48608): (cancer susceptibility 16)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03064	NR_184325.1	n.215T>C		non_coding_transcript_exon_variant	Exon 1 of 3
LINC03064	NR_184326.1	n.215T>C		non_coding_transcript_exon_variant	Exon 1 of 3
LINC03064	NR_184331.1	n.215T>C		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03064	ENST00000564361.2	n.208T>C		non_coding_transcript_exon_variant	Exon 1 of 3	3
LINC03064	ENST00000565153.2	n.253T>C		non_coding_transcript_exon_variant	Exon 1 of 3	2
LINC03064	ENST00000655643.1	n.223T>C		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75202 AN: 151964 Hom.: 19422 Cov.: 33

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.532

GnomAD4 exome AF: 0.443 AC: 148 AN: 334 Hom.: 33 AF XY: 0.437 AC XY: 76 AN XY: 174

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 2 AN: 4

East Asian (EAS) AF: 0.750 AC: 21 AN: 28

South Asian (SAS) AF: 0.500 AC: 2 AN: 4

European-Finnish (FIN) AF: 0.375 AC: 24 AN: 64

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.415 AC: 88 AN: 212

Other (OTH) AF: 0.375 AC: 6 AN: 16

GnomAD4 genome AF: 0.495 AC: 75300 AN: 152082 Hom.: 19465 Cov.: 33 AF XY: 0.493 AC XY: 36624 AN XY: 74332

African (AFR) AF: 0.584 AC: 24217 AN: 41480

American (AMR) AF: 0.557 AC: 8520 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1894 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4052 AN: 5166

South Asian (SAS) AF: 0.460 AC: 2215 AN: 4820

European-Finnish (FIN) AF: 0.363 AC: 3836 AN: 10576

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28819 AN: 67964

Other (OTH) AF: 0.536 AC: 1135 AN: 2116

Alfa AF: 0.456 Hom.: 9821

Bravo AF: 0.514

Asia WGS AF: 0.595 AC: 2073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.72
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs3104793; hg19: chr16-52641186; COSMIC: COSV72520837;