13-108437268-G-A

Variant names:

• chr13-108437268-G-A
• rs9587583
• ENST00000636252.1:n.334-9914G>A

Variant summary

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

The ENST00000636252.1(ENSG00000283384):​n.334-9914G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0883 in 152,146 control chromosomes in the GnomAD database, including 613 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 0.088 (613 hom., cov: 32)
• Consequence: ENSG00000283384 ENST00000636252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 1 publications found

Genes affected

ENSG00000283384 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636252.1. 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
	ENSG00000283384	ENST00000636252.1	TSL:5	n.334-9914G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0884 AC: 13432 AN: 152028 Hom.: 613 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.0925

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.0883

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.0920

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

GnomAD4 genome AF: 0.0883 AC: 13435 AN: 152146 Hom.: 613 Cov.: 32 AF XY: 0.0862 AC XY: 6412 AN XY: 74378

African (AFR) AF: 0.108 AC: 4484 AN: 41514

American (AMR) AF: 0.0613 AC: 937 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0893 AC: 310 AN: 3472

East Asian (EAS) AF: 0.0927 AC: 479 AN: 5168

South Asian (SAS) AF: 0.0637 AC: 307 AN: 4822

European-Finnish (FIN) AF: 0.0883 AC: 935 AN: 10586

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0834 AC: 5673 AN: 67996

Other (OTH) AF: 0.0920 AC: 194 AN: 2108

Alfa AF: 0.0810 Hom.: 849

Bravo AF: 0.0878

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.94
DANN	Benign	0.33
PhyloP100		-0.35

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: rs9587583;

hg19: chr13-109089616;