6-30569829-C-G

Variant names:

• chr6-30569829-C-G
• rs3132613
• ENST00000832105.1:n.187+1163G>C

Variant summary

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

The ENST00000832105.1(ENSG00000290047):​n.187+1163G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,164 control chromosomes in the GnomAD database, including 40,607 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 0.73 (40607 hom., cov: 33)
• Consequence: ENSG00000290047 ENST00000832105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 33 publications found

Genes affected

ENSG00000290047 (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 (AFR) allele frequency at 95% confidence interval = 0.828 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
ENSG00000290047	ENST00000832105.1	n.187+1163G>C		intron_variant	Intron 2 of 2
ENSG00000290047	ENST00000832106.1	n.179+1163G>C		intron_variant	Intron 2 of 3
ENSG00000290047	ENST00000832107.1	n.188+1163G>C		intron_variant	Intron 2 of 2
ENSG00000290047	ENST00000832108.1	n.282+1163G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110521 AN: 152046 Hom.: 40562 Cov.: 33

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.727 AC: 110624 AN: 152164 Hom.: 40607 Cov.: 33 AF XY: 0.724 AC XY: 53853 AN XY: 74376

African (AFR) AF: 0.836 AC: 34715 AN: 41536

American (AMR) AF: 0.649 AC: 9914 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2846 AN: 3472

East Asian (EAS) AF: 0.697 AC: 3603 AN: 5172

South Asian (SAS) AF: 0.827 AC: 3993 AN: 4828

European-Finnish (FIN) AF: 0.678 AC: 7161 AN: 10566

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45954 AN: 68000

Other (OTH) AF: 0.727 AC: 1533 AN: 2110

Alfa AF: 0.686 Hom.: 17594

Bravo AF: 0.730

Asia WGS AF: 0.779 AC: 2710 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	1.2
DANN	Benign	0.31
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs3132613; hg19: chr6-30537606;