rs13253111

Variant names:

• chr8-28204457-A-G
• rs13253111
• ENST00000842508.1:n.220-21924T>C

Variant summary

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

The ENST00000842508.1(ENSG00000309630):​n.220-21924T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,134 control chromosomes in the GnomAD database, including 11,266 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 0.37 (11266 hom., cov: 32)
• Consequence: ENSG00000309630 ENST00000842508.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 15 publications found

Genes affected

ENSG00000309630 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 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
ENSG00000309630	ENST00000842508.1	n.220-21924T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55681 AN: 152016 Hom.: 11264 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.366 AC: 55709 AN: 152134 Hom.: 11266 Cov.: 32 AF XY: 0.366 AC XY: 27183 AN XY: 74366

African (AFR) AF: 0.189 AC: 7863 AN: 41526

American (AMR) AF: 0.394 AC: 6015 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3468

East Asian (EAS) AF: 0.545 AC: 2821 AN: 5178

South Asian (SAS) AF: 0.415 AC: 2002 AN: 4820

European-Finnish (FIN) AF: 0.368 AC: 3886 AN: 10566

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

European-Non Finnish (NFE) AF: 0.444 AC: 30194 AN: 67984

Other (OTH) AF: 0.401 AC: 845 AN: 2108

Alfa AF: 0.422 Hom.: 7748

Bravo AF: 0.365

Asia WGS AF: 0.472 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs13253111; hg19: chr8-28061974;