chr5-56683302-A-C

Variant names:

• chr5-56683302-A-C
• rs13362504
• ENST00000821819.1:n.62-6774T>G

Variant summary

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

The ENST00000821819.1(ENSG00000306891):​n.62-6774T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,962 control chromosomes in the GnomAD database, including 6,701 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 (6701 hom., cov: 32)
• Consequence: ENSG00000306891 ENST00000821819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.899
• Publications: 0 publications found

Genes affected

ENSG00000306891 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821819.1. 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
	ENSG00000306891	ENST00000821819.1		n.62-6774T>G		intron	N/A
	ENSG00000306891	ENST00000821820.1		n.94-648T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43337 AN: 151844 Hom.: 6691 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.285 AC: 43375 AN: 151962 Hom.: 6701 Cov.: 32 AF XY: 0.287 AC XY: 21355 AN XY: 74288

African (AFR) AF: 0.399 AC: 16515 AN: 41418

American (AMR) AF: 0.354 AC: 5394 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3464

East Asian (EAS) AF: 0.237 AC: 1226 AN: 5170

South Asian (SAS) AF: 0.276 AC: 1330 AN: 4814

European-Finnish (FIN) AF: 0.217 AC: 2292 AN: 10570

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14885 AN: 67954

Other (OTH) AF: 0.291 AC: 614 AN: 2108

Alfa AF: 0.249 Hom.: 2603

Bravo AF: 0.305

Asia WGS AF: 0.224 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.2
DANN	Benign	0.74
PhyloP100		0.90

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: rs13362504;

hg19: chr5-55979129;