rs3104792

Variant names:

• chr16-52607098-T-A
• rs3104792
• ENST00000564361.2:n.32T>A

Variant summary

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

The ENST00000564361.2(LINC03064):​n.32T>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 0.0145 in 152,324 control chromosomes in the GnomAD database, including 64 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 0.014 (64 hom., cov: 32)
• Consequence: LINC03064 ENST00000564361.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.682
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03064	NR_184325.1	n.39T>A		non_coding_transcript_exon_variant	Exon 1 of 3
LINC03064	NR_184326.1	n.39T>A		non_coding_transcript_exon_variant	Exon 1 of 3
LINC03064	NR_184327.1	n.39T>A		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.32T>A		non_coding_transcript_exon_variant	Exon 1 of 3	3
LINC03064	ENST00000565153.2	n.77T>A		non_coding_transcript_exon_variant	Exon 1 of 3	2
LINC03064	ENST00000655643.1	n.47T>A		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0144 AC: 2199 AN: 152206 Hom.: 64 Cov.: 32

Gnomad AFR AF: 0.00673

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0137

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0485

Gnomad FIN AF: 0.0242

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00423

Gnomad OTH AF: 0.0215

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0145 AC: 2205 AN: 152324 Hom.: 64 Cov.: 32 AF XY: 0.0166 AC XY: 1234 AN XY: 74486

African (AFR) AF: 0.00673 AC: 280 AN: 41578

American (AMR) AF: 0.0137 AC: 210 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0317 AC: 110 AN: 3472

East Asian (EAS) AF: 0.145 AC: 752 AN: 5176

South Asian (SAS) AF: 0.0487 AC: 235 AN: 4824

European-Finnish (FIN) AF: 0.0242 AC: 257 AN: 10626

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00423 AC: 288 AN: 68026

Other (OTH) AF: 0.0213 AC: 45 AN: 2116

Alfa AF: 0.00900 Hom.: 2

Bravo AF: 0.0143

Asia WGS AF: 0.0800 AC: 276 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.51
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs3104792; hg19: chr16-52641010;