6-30454855-A-G

Variant names:

• chr6-30454855-A-G
• rs2844729
• ENST00000658719.1:n.1839A>G

Variant summary

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

The ENST00000658719.1(ENSG00000286301):​n.1839A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,050 control chromosomes in the GnomAD database, including 30,752 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 (30752 hom., cov: 32)
• Consequence: ENSG00000286301 ENST00000658719.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853
• Publications: 25 publications found

Genes affected

ENSG00000286301 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286301	ENST00000658719.1	n.1839A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96263 AN: 151932 Hom.: 30720 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.634 AC: 96352 AN: 152050 Hom.: 30752 Cov.: 32 AF XY: 0.634 AC XY: 47080 AN XY: 74300

African (AFR) AF: 0.669 AC: 27743 AN: 41456

American (AMR) AF: 0.621 AC: 9488 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2400 AN: 3468

East Asian (EAS) AF: 0.799 AC: 4139 AN: 5180

South Asian (SAS) AF: 0.716 AC: 3454 AN: 4822

European-Finnish (FIN) AF: 0.631 AC: 6669 AN: 10568

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40342 AN: 67956

Other (OTH) AF: 0.628 AC: 1327 AN: 2112

Alfa AF: 0.613 Hom.: 105981

Bravo AF: 0.637

Asia WGS AF: 0.744 AC: 2586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.50
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs2844729; hg19: chr6-30422632;