5-123821728-A-G

Variant names:

• chr5-123821728-A-G
• rs257016
• ENST00000744066.1:n.68-3082A>G

Variant summary

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

The ENST00000744066.1(ENSG00000296985):​n.68-3082A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 151,984 control chromosomes in the GnomAD database, including 42,171 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 0.73 (42171 hom., cov: 31)
• Consequence: ENSG00000296985 ENST00000744066.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912
• Publications: 8 publications found

Genes affected

ENSG00000296985 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744066.1. 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
	ENSG00000296985	ENST00000744066.1		n.68-3082A>G		intron	N/A
	ENSG00000296985	ENST00000744067.1		n.123-3082A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111434 AN: 151868 Hom.: 42108 Cov.: 31

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.734 AC: 111555 AN: 151984 Hom.: 42171 Cov.: 31 AF XY: 0.742 AC XY: 55065 AN XY: 74234

African (AFR) AF: 0.879 AC: 36437 AN: 41472

American (AMR) AF: 0.733 AC: 11187 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2094 AN: 3470

East Asian (EAS) AF: 0.980 AC: 5056 AN: 5160

South Asian (SAS) AF: 0.813 AC: 3914 AN: 4814

European-Finnish (FIN) AF: 0.724 AC: 7634 AN: 10538

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43266 AN: 67950

Other (OTH) AF: 0.689 AC: 1453 AN: 2108

Alfa AF: 0.676 Hom.: 73224

Bravo AF: 0.739

Asia WGS AF: 0.890 AC: 3096 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	0.64
DANN	Benign	0.33
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs257016; hg19: chr5-123157422;