chr4-122825464-A-C

Variant names:

• chr4-122825464-A-C
• rs308393
• ENST00000779266.1:n.464A>C

Variant summary

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

The ENST00000779266.1(ENSG00000301488):​n.464A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,128 control chromosomes in the GnomAD database, including 9,704 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 (9704 hom., cov: 32)
• Consequence: ENSG00000301488 ENST00000779266.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 4 publications found

Genes affected

ENSG00000301488 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779266.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301488	ENST00000779266.1		n.464A>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43769 AN: 152008 Hom.: 9667 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.288 AC: 43864 AN: 152128 Hom.: 9704 Cov.: 32 AF XY: 0.286 AC XY: 21282 AN XY: 74378

African (AFR) AF: 0.615 AC: 25481 AN: 41454

American (AMR) AF: 0.240 AC: 3665 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3472

East Asian (EAS) AF: 0.126 AC: 654 AN: 5186

South Asian (SAS) AF: 0.339 AC: 1627 AN: 4806

European-Finnish (FIN) AF: 0.125 AC: 1330 AN: 10602

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9593 AN: 68004

Other (OTH) AF: 0.275 AC: 580 AN: 2110

Alfa AF: 0.207 Hom.: 677

Bravo AF: 0.309

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.29
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs308393; hg19: chr4-123746619;