21-45235470-G-A

Position:

• chr21-45235470-G-A

Variant summary

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

The ENST00000328344.2(LINC00334):​n.155+964G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,148 control chromosomes in the GnomAD database, including 1,219 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 0.11 (1219 hom., cov: 32)
• Consequence: LINC00334 ENST00000328344.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

Genes affected

LINC00334 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00334	NR_135279.1	n.167+964G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00334	ENST00000328344.2	n.155+964G>A		intron_variant		2
LINC00334	ENST00000584169.5	n.137+994G>A		intron_variant		4
LINC00334	ENST00000638500.1	n.137+994G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16435 AN: 152030 Hom.: 1214 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0968

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0492

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0532

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.108 AC: 16472 AN: 152148 Hom.: 1219 Cov.: 32 AF XY: 0.109 AC XY: 8072 AN XY: 74382

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.0972

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0492

Gnomad4 NFE AF: 0.0532

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0685 Hom.: 636

Bravo AF: 0.117

Asia WGS AF: 0.210 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.56
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2838824; hg19: chr21-46655385;