rs218869

Variant names:

• chr8-23778768-T-A
• rs218869
• ENST00000523874.1:n.76-9725T>A

Variant summary

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

The ENST00000523874.1(ENSG00000253471):​n.76-9725T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,098 control chromosomes in the GnomAD database, including 40,416 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 0.72 (40416 hom., cov: 32)
• Consequence: ENSG00000253471 ENST00000523874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 1 publications found

Genes affected

ENSG00000253471 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986930	XR_001745842.2	n.1313-9725T>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253471	ENST00000523874.1	n.76-9725T>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109564 AN: 151978 Hom.: 40385 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.721 AC: 109651 AN: 152098 Hom.: 40416 Cov.: 32 AF XY: 0.726 AC XY: 54001 AN XY: 74346

African (AFR) AF: 0.571 AC: 23666 AN: 41442

American (AMR) AF: 0.747 AC: 11412 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2567 AN: 3468

East Asian (EAS) AF: 0.560 AC: 2886 AN: 5158

South Asian (SAS) AF: 0.768 AC: 3710 AN: 4828

European-Finnish (FIN) AF: 0.888 AC: 9424 AN: 10608

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53552 AN: 67992

Other (OTH) AF: 0.740 AC: 1565 AN: 2116

Alfa AF: 0.762 Hom.: 5566

Bravo AF: 0.700

Asia WGS AF: 0.697 AC: 2419 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.45
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs218869; hg19: chr8-23636281;