rs375555

Variant names:

• chr6-33589964-T-C
• rs375555
• ENST00000477984.1:n.343-2094A>G

Variant summary

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

The ENST00000477984.1(LINC00336):​n.343-2094A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,224 control chromosomes in the GnomAD database, including 3,366 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 0.20 (3366 hom., cov: 33)
• Consequence: LINC00336 ENST00000477984.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964
• Publications: 20 publications found

Genes affected

LINC00336 (HGNC:33813): (long intergenic non-protein coding RNA 336)

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 = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00336	NR_027908.2	n.343-2094A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00336	ENST00000477984.1	n.343-2094A>G		intron_variant	Intron 1 of 1	2
LINC00336	ENST00000689377.2	n.342+3033A>G		intron_variant	Intron 1 of 1
LINC00336	ENST00000738200.1	n.348+3033A>G		intron_variant	Intron 2 of 2
LINC00336	ENST00000738201.1	n.410+2123A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29976 AN: 152106 Hom.: 3360 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.197 AC: 29987 AN: 152224 Hom.: 3366 Cov.: 33 AF XY: 0.200 AC XY: 14888 AN XY: 74432

African (AFR) AF: 0.144 AC: 5960 AN: 41530

American (AMR) AF: 0.213 AC: 3262 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 721 AN: 3472

East Asian (EAS) AF: 0.458 AC: 2368 AN: 5168

South Asian (SAS) AF: 0.367 AC: 1770 AN: 4822

European-Finnish (FIN) AF: 0.155 AC: 1646 AN: 10610

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13494 AN: 67994

Other (OTH) AF: 0.238 AC: 503 AN: 2114

Alfa AF: 0.205 Hom.: 11236

Bravo AF: 0.196

Asia WGS AF: 0.442 AC: 1539 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	0.71
DANN	Benign	0.72
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs375555; hg19: chr6-33557741;