chr13-62202300-A-C

Variant names:

• chr13-62202300-A-C
• rs9285235
• ENST00000792229.1:n.259-8872T>G

Variant summary

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

The ENST00000792229.1(ENSG00000303156):​n.259-8872T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,932 control chromosomes in the GnomAD database, including 19,191 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 0.50 (19191 hom., cov: 33)
• Consequence: ENSG00000303156 ENST00000792229.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648
• Publications: 3 publications found

Genes affected

ENSG00000303156 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792229.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303156	ENST00000792229.1		n.259-8872T>G		intron	N/A
	ENSG00000303156	ENST00000792230.1		n.259-8872T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75553 AN: 151814 Hom.: 19183 Cov.: 33

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.497 AC: 75579 AN: 151932 Hom.: 19191 Cov.: 33 AF XY: 0.489 AC XY: 36310 AN XY: 74254

African (AFR) AF: 0.416 AC: 17225 AN: 41452

American (AMR) AF: 0.516 AC: 7878 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1801 AN: 3464

East Asian (EAS) AF: 0.438 AC: 2266 AN: 5172

South Asian (SAS) AF: 0.388 AC: 1868 AN: 4820

European-Finnish (FIN) AF: 0.398 AC: 4207 AN: 10566

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.572 AC: 38848 AN: 67886

Other (OTH) AF: 0.517 AC: 1089 AN: 2106

Alfa AF: 0.387 Hom.: 1099

Bravo AF: 0.502

Asia WGS AF: 0.441 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.49
PhyloP100		0.65

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9285235;

hg19: chr13-62776433;