8-124729925-A-G

Variant names:

• chr8-124729925-A-G
• rs891541
• ENST00000811280.1:n.469A>G

Variant summary

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

The ENST00000811280.1(ENSG00000305490):​n.469A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,084 control chromosomes in the GnomAD database, including 35,949 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 0.68 (35949 hom., cov: 32)
• Consequence: ENSG00000305490 ENST00000811280.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 4 publications found

Genes affected

ENSG00000305490 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811280.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305490	ENST00000811280.1		n.469A>G		splice_region non_coding_transcript_exon	Exon 1 of 4
	ENSG00000305490	ENST00000811281.1		n.1265A>G		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000305490	ENST00000811284.1		n.1159A>G		splice_region non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103573 AN: 151966 Hom.: 35913 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.682 AC: 103665 AN: 152084 Hom.: 35949 Cov.: 32 AF XY: 0.681 AC XY: 50655 AN XY: 74344

African (AFR) AF: 0.560 AC: 23230 AN: 41450

American (AMR) AF: 0.779 AC: 11913 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2316 AN: 3468

East Asian (EAS) AF: 0.574 AC: 2960 AN: 5160

South Asian (SAS) AF: 0.584 AC: 2816 AN: 4826

European-Finnish (FIN) AF: 0.734 AC: 7762 AN: 10568

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.739 AC: 50266 AN: 68002

Other (OTH) AF: 0.712 AC: 1505 AN: 2114

Alfa AF: 0.726 Hom.: 50416

Bravo AF: 0.683

Asia WGS AF: 0.613 AC: 2133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.87
DANN	Benign	0.51
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs891541; hg19: chr8-125742166;