rs4242539

Variant names:

• chr8-1746070-A-G
• rs4242539
• ENST00000727728.1:n.356A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-1746070-A-G
• chr8-1746070-A-T

Variant summary

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

The ENST00000727728.1(ENSG00000295066):​n.356A>G 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 0.742 in 152,200 control chromosomes in the GnomAD database, including 42,184 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 0.74 (42184 hom., cov: 33)
• Consequence: ENSG00000295066 ENST00000727728.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 5 publications found

Genes affected

ENSG00000295066 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727728.1. 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
	ENSG00000295066	ENST00000727728.1		n.356A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000295066	ENST00000727729.1		n.364A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000295026	ENST00000727493.1		n.602+2224T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112889 AN: 152082 Hom.: 42158 Cov.: 33

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.742 AC: 112963 AN: 152200 Hom.: 42184 Cov.: 33 AF XY: 0.742 AC XY: 55237 AN XY: 74408

African (AFR) AF: 0.715 AC: 29665 AN: 41510

American (AMR) AF: 0.642 AC: 9809 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2564 AN: 3470

East Asian (EAS) AF: 0.764 AC: 3964 AN: 5186

South Asian (SAS) AF: 0.786 AC: 3792 AN: 4822

European-Finnish (FIN) AF: 0.787 AC: 8340 AN: 10598

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52285 AN: 68004

Other (OTH) AF: 0.755 AC: 1597 AN: 2116

Alfa AF: 0.748 Hom.: 49581

Bravo AF: 0.727

Asia WGS AF: 0.777 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.065
DANN	Benign	0.36
PhyloP100		-1.7

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: rs4242539;

hg19: chr8-1694236;