chr5-55833600-A-G

Variant names:

• chr5-55833600-A-G
• rs162096
• ENST00000816389.1:n.114-5925A>G

Variant summary

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

The ENST00000816389.1(ENSG00000306236):​n.114-5925A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,186 control chromosomes in the GnomAD database, including 6,002 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 0.26 (6002 hom., cov: 32)
• Consequence: ENSG00000306236 ENST00000816389.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565
• Publications: 1 publications found

Genes affected

ENSG00000306236 (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 = 0.507 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816389.1. 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
	ENSG00000306236	ENST00000816389.1		n.114-5925A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39907 AN: 152068 Hom.: 5989 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.263 AC: 39966 AN: 152186 Hom.: 6002 Cov.: 32 AF XY: 0.262 AC XY: 19484 AN XY: 74442

African (AFR) AF: 0.330 AC: 13699 AN: 41508

American (AMR) AF: 0.390 AC: 5961 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2715 AN: 5182

South Asian (SAS) AF: 0.205 AC: 990 AN: 4826

European-Finnish (FIN) AF: 0.154 AC: 1637 AN: 10602

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13583 AN: 67992

Other (OTH) AF: 0.247 AC: 520 AN: 2108

Alfa AF: 0.211 Hom.: 3562

Bravo AF: 0.291

Asia WGS AF: 0.337 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		0.56

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: rs162096;

hg19: chr5-55129428;