chr8-1746070-A-G

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377778	XR_001745757.1	n.695+2224T>C		intron_variant	Intron 2 of 2
LOC105377778	XR_007060784.1	n.649+2224T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295066	ENST00000727728.1	n.356A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000295066	ENST00000727729.1	n.364A>G		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000295026	ENST00000727493.1	n.602+2224T>C		intron_variant	Intron 4 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs4242539; hg19: chr8-1694236;