rs6543297

Variant names:

• chr2-105454702-C-T
• rs6543297
• ENST00000760277.1:n.344-786G>A

Variant summary

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

The ENST00000760277.1(ENSG00000299064):​n.344-786G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 152,066 control chromosomes in the GnomAD database, including 30,458 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 0.63 (30458 hom., cov: 33)
• Consequence: ENSG00000299064 ENST00000760277.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680
• Publications: 3 publications found

Genes affected

ENSG00000299064 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373529	XR_923141.1	n.-11G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299064	ENST00000760277.1	n.344-786G>A		intron_variant	Intron 1 of 2
ENSG00000299064	ENST00000760278.1	n.344-786G>A		intron_variant	Intron 1 of 1
ENSG00000299064	ENST00000760279.1	n.117-786G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95941 AN: 151948 Hom.: 30415 Cov.: 33

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.632 AC: 96040 AN: 152066 Hom.: 30458 Cov.: 33 AF XY: 0.628 AC XY: 46699 AN XY: 74318

African (AFR) AF: 0.616 AC: 25561 AN: 41470

American (AMR) AF: 0.595 AC: 9100 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2589 AN: 3468

East Asian (EAS) AF: 0.682 AC: 3520 AN: 5158

South Asian (SAS) AF: 0.596 AC: 2872 AN: 4822

European-Finnish (FIN) AF: 0.583 AC: 6160 AN: 10570

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44020 AN: 67966

Other (OTH) AF: 0.650 AC: 1376 AN: 2116

Alfa AF: 0.648 Hom.: 48214

Bravo AF: 0.632

Asia WGS AF: 0.624 AC: 2171 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	1.3
DANN	Benign	0.44
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs6543297; hg19: chr2-106071159;