chr5-121233413-G-A

Variant names:

• chr5-121233413-G-A
• rs4895298
• ENST00000599562.5:n.228+28283G>A

Variant summary

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

The ENST00000661647.1(ENSG00000229855):​n.195+68532G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,034 control chromosomes in the GnomAD database, including 45,758 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 0.77 (45758 hom., cov: 32)
• Consequence: ENSG00000229855 ENST00000661647.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 1 publications found

Genes affected

ENSG00000229855 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661647.1. 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
	ENSG00000229855	ENST00000599562.5	TSL:5	n.228+28283G>A		intron	N/A
	ENSG00000229855	ENST00000661647.1		n.195+68532G>A		intron	N/A
	ENSG00000229855	ENST00000767774.1		n.85+68532G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116447 AN: 151916 Hom.: 45749 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.766 AC: 116498 AN: 152034 Hom.: 45758 Cov.: 32 AF XY: 0.766 AC XY: 56949 AN XY: 74340

African (AFR) AF: 0.583 AC: 24146 AN: 41416

American (AMR) AF: 0.776 AC: 11857 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3185 AN: 3470

East Asian (EAS) AF: 0.682 AC: 3524 AN: 5168

South Asian (SAS) AF: 0.861 AC: 4151 AN: 4822

European-Finnish (FIN) AF: 0.820 AC: 8681 AN: 10588

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58157 AN: 67980

Other (OTH) AF: 0.783 AC: 1655 AN: 2114

Alfa AF: 0.829 Hom.: 166921

Bravo AF: 0.753

Asia WGS AF: 0.764 AC: 2652 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.82
DANN	Benign	0.81
PhyloP100		-1.1

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: rs4895298;

hg19: chr5-120569108;