13-85777273-A-G

Variant names:

• chr13-85777273-A-G
• rs623412
• ENST00000647840.1:n.378+5553T>C

Variant summary

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

The ENST00000647840.1(ENSG00000285834):​n.378+5553T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,962 control chromosomes in the GnomAD database, including 7,128 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 0.29 (7128 hom., cov: 33)
• Consequence: ENSG00000285834 ENST00000647840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423
• Publications: 1 publications found

Genes affected

ENSG00000285834 (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 (EAS) allele frequency at 95% confidence interval = 0.617 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
ENSG00000285834	ENST00000647840.1	n.378+5553T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44103 AN: 151838 Hom.: 7120 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.290 AC: 44140 AN: 151962 Hom.: 7128 Cov.: 33 AF XY: 0.291 AC XY: 21647 AN XY: 74286

African (AFR) AF: 0.190 AC: 7872 AN: 41500

American (AMR) AF: 0.387 AC: 5900 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1050 AN: 3470

East Asian (EAS) AF: 0.635 AC: 3277 AN: 5160

South Asian (SAS) AF: 0.351 AC: 1687 AN: 4812

European-Finnish (FIN) AF: 0.232 AC: 2455 AN: 10566

Middle Eastern (MID) AF: 0.259 AC: 73 AN: 282

European-Non Finnish (NFE) AF: 0.309 AC: 20971 AN: 67894

Other (OTH) AF: 0.319 AC: 671 AN: 2102

Alfa AF: 0.285 Hom.: 861

Bravo AF: 0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.74
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs623412; hg19: chr13-86351408;