rs209181

Variant names:

• chr6-28824700-G-A
• rs209181
• ENST00000829044.1:n.695-226G>A

Variant summary

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

The ENST00000829044.1(ENSG00000307816):​n.695-226G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 151,986 control chromosomes in the GnomAD database, including 1,307 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 0.13 (1307 hom., cov: 30)
• Consequence: ENSG00000307816 ENST00000829044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 26 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=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 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.695-226G>A		intron_variant	Intron 2 of 2
ENSG00000307816	ENST00000829045.1	n.404-226G>A		intron_variant	Intron 4 of 4
ENSG00000307816	ENST00000829046.1	n.281-226G>A		intron_variant	Intron 3 of 3
ENSG00000307816	ENST00000829047.1	n.137-226G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19075 AN: 151868 Hom.: 1306 Cov.: 30

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.0827

Gnomad FIN AF: 0.0813

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.126 AC: 19086 AN: 151986 Hom.: 1307 Cov.: 30 AF XY: 0.120 AC XY: 8913 AN XY: 74292

African (AFR) AF: 0.157 AC: 6490 AN: 41446

American (AMR) AF: 0.0692 AC: 1055 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0779 AC: 270 AN: 3466

East Asian (EAS) AF: 0.0200 AC: 103 AN: 5154

South Asian (SAS) AF: 0.0825 AC: 398 AN: 4822

European-Finnish (FIN) AF: 0.0813 AC: 859 AN: 10560

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9511 AN: 67968

Other (OTH) AF: 0.110 AC: 232 AN: 2110

Alfa AF: 0.137 Hom.: 4358

Bravo AF: 0.127

Asia WGS AF: 0.0550 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	4.9
DANN	Benign	0.83
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs209181; hg19: chr6-28792477;