rs375555

chr6-33589964-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027908.2(LINC00336):n.343-2094A>G variant causes a intron, non coding transcript 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 NR_027908.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00336	NR_027908.2	n.343-2094A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00336	ENST00000477984.1	n.343-2094A>G		intron_variant, non_coding_transcript_variant		2
LINC00336	ENST00000689377.1	n.320+3033A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.238

Alfa AF: 0.209 Hom.: 7493

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs375555; hg19: chr6-33557741;