3-546765-A-G

Position:

• chr3-546765-A-G

Variant summary

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

The ENST00000657004.1(ENSG00000287505):​n.149+4744T>C 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 0.114 in 152,124 control chromosomes in the GnomAD database, including 3,026 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 (3026 hom., cov: 32)
• Consequence: ENST00000657004.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

Genes affected

(HGNC:):

LINC01266 (HGNC:50309): (long intergenic non-protein coding RNA 1266)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000657004.1	n.149+4744T>C		intron_variant, non_coding_transcript_variant
LINC01266	ENST00000661103.1	n.266+10438A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17360 AN: 152006 Hom.: 3013 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0518

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0190

Gnomad FIN AF: 0.00170

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.00978

Gnomad OTH AF: 0.0867

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

GnomAD4 genome AF: 0.114 AC: 17411 AN: 152124 Hom.: 3026 Cov.: 32 AF XY: 0.112 AC XY: 8364 AN XY: 74386

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.0517

Gnomad4 ASJ AF: 0.0115

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0190

Gnomad4 FIN AF: 0.00170

Gnomad4 NFE AF: 0.00978

Gnomad4 OTH AF: 0.0858

Alfa AF: 0.0465 Hom.: 425

Bravo AF: 0.130

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6778854; hg19: chr3-588448;