13-46814392-C-T

Variant names:

• chr13-46814392-C-T
• rs9526236
• ENST00000783844.1:n.95+16428C>T

Variant summary

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

The ENST00000783844.1(ENSG00000302073):​n.95+16428C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,606 control chromosomes in the GnomAD database, including 15,398 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 0.45 (15398 hom., cov: 32)
• Consequence: ENSG00000302073 ENST00000783844.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 4 publications found

Genes affected

ENSG00000302073 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783844.1. 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
	ENSG00000302073	ENST00000783844.1		n.95+16428C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67551 AN: 151490 Hom.: 15397 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.446 AC: 67566 AN: 151606 Hom.: 15398 Cov.: 32 AF XY: 0.436 AC XY: 32286 AN XY: 74078

African (AFR) AF: 0.471 AC: 19501 AN: 41368

American (AMR) AF: 0.403 AC: 6138 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1967 AN: 3464

East Asian (EAS) AF: 0.309 AC: 1598 AN: 5164

South Asian (SAS) AF: 0.218 AC: 1048 AN: 4800

European-Finnish (FIN) AF: 0.354 AC: 3697 AN: 10454

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32070 AN: 67828

Other (OTH) AF: 0.452 AC: 954 AN: 2110

Alfa AF: 0.446 Hom.: 2133

Bravo AF: 0.456

Asia WGS AF: 0.268 AC: 929 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.41
PhyloP100		-2.3

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: rs9526236;

hg19: chr13-47388527;

COSMIC: COSV65945769;