ENST00000636252.1:n.333+31339G>A

Variant names:

• chr13-108406051-G-A
• rs725122
• ENST00000636252.1:n.333+31339G>A

Variant summary

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

The ENST00000636252.1(ENSG00000283384):​n.333+31339G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0816 in 152,200 control chromosomes in the GnomAD database, including 718 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 0.082 (718 hom., cov: 32)
• Consequence: ENSG00000283384 ENST00000636252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.249 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
ENSG00000283384	ENST00000636252.1	n.333+31339G>A		intron_variant	Intron 3 of 3	5
ENSG00000283384	ENST00000637731.1	n.476-25420G>A		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12406 AN: 152082 Hom.: 715 Cov.: 32

Gnomad AFR AF: 0.0373

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0714

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0761

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.0816 AC: 12416 AN: 152200 Hom.: 718 Cov.: 32 AF XY: 0.0841 AC XY: 6257 AN XY: 74404

African (AFR) AF: 0.0372 AC: 1546 AN: 41514

American (AMR) AF: 0.155 AC: 2373 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0640 AC: 222 AN: 3470

East Asian (EAS) AF: 0.260 AC: 1342 AN: 5160

South Asian (SAS) AF: 0.155 AC: 748 AN: 4828

European-Finnish (FIN) AF: 0.0714 AC: 758 AN: 10616

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0761 AC: 5178 AN: 68010

Other (OTH) AF: 0.0980 AC: 207 AN: 2112

Alfa AF: 0.0778 Hom.: 962

Bravo AF: 0.0855

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.55
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs725122; hg19: chr13-109058399;