6-28808205-G-C

Variant names:

• chr6-28808205-G-C
• rs1011094
• ENST00000829044.1:n.694+4931G>C

Variant summary

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

The ENST00000829044.1(ENSG00000307816):​n.694+4931G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,058 control chromosomes in the GnomAD database, including 24,528 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 0.56 (24528 hom., cov: 32)
• Consequence: ENSG00000307816 ENST00000829044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 5 publications found

Genes affected

ENSG00000307816 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 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
ENSG00000307816	ENST00000829044.1	n.694+4931G>C		intron_variant	Intron 2 of 2
ENSG00000307816	ENST00000829045.1	n.403+4931G>C		intron_variant	Intron 4 of 4
ENSG00000307816	ENST00000829046.1	n.280+4931G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84387 AN: 151940 Hom.: 24483 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.556 AC: 84484 AN: 152058 Hom.: 24528 Cov.: 32 AF XY: 0.553 AC XY: 41121 AN XY: 74324

African (AFR) AF: 0.720 AC: 29854 AN: 41492

American (AMR) AF: 0.538 AC: 8218 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1785 AN: 3472

East Asian (EAS) AF: 0.631 AC: 3256 AN: 5162

South Asian (SAS) AF: 0.540 AC: 2604 AN: 4824

European-Finnish (FIN) AF: 0.406 AC: 4286 AN: 10544

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32613 AN: 67974

Other (OTH) AF: 0.541 AC: 1141 AN: 2108

Alfa AF: 0.501 Hom.: 2462

Bravo AF: 0.577

Asia WGS AF: 0.543 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.54
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1011094; hg19: chr6-28775982;