8-109043458-T-C

Variant names:

• chr8-109043458-T-C
• rs6469224
• ENST00000522244.1:n.264+219A>G

Variant summary

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

The ENST00000522244.1(ENSG00000253796):​n.264+219A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,058 control chromosomes in the GnomAD database, including 29,114 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 0.61 (29114 hom., cov: 32)
• Consequence: ENSG00000253796 ENST00000522244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 1 publications found

Genes affected

ENSG00000253796 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 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
ENSG00000253796	ENST00000522244.1	n.264+219A>G		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93298 AN: 151940 Hom.: 29078 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.614 AC: 93389 AN: 152058 Hom.: 29114 Cov.: 32 AF XY: 0.616 AC XY: 45754 AN XY: 74330

African (AFR) AF: 0.686 AC: 28449 AN: 41480

American (AMR) AF: 0.708 AC: 10830 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1833 AN: 3470

East Asian (EAS) AF: 0.716 AC: 3679 AN: 5136

South Asian (SAS) AF: 0.605 AC: 2914 AN: 4818

European-Finnish (FIN) AF: 0.536 AC: 5668 AN: 10574

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37960 AN: 67974

Other (OTH) AF: 0.602 AC: 1272 AN: 2114

Alfa AF: 0.593 Hom.: 3530

Bravo AF: 0.633

Asia WGS AF: 0.668 AC: 2323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.72
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs6469224; hg19: chr8-110055687;