ENST00000656790.1:n.729A>G

Variant names:

• chr8-85975134-T-C
• rs1946380
• ENST00000656790.1:n.729A>G

Variant summary

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

The ENST00000656790.1(ENSG00000287927):​n.729A>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 0.0887 in 152,088 control chromosomes in the GnomAD database, including 1,209 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 0.089 (1209 hom., cov: 32)
• Consequence: ENSG00000287927 ENST00000656790.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• Publications: 0 publications found

Genes affected

ENSG00000287927 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986954	XR_001745984.1	n.942A>G		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287927	ENST00000656790.1	n.729A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000287927	ENST00000751425.1	n.814A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0885 AC: 13452 AN: 151970 Hom.: 1201 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0480

Gnomad ASJ AF: 0.0355

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.0486

Gnomad FIN AF: 0.0631

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0252

Gnomad OTH AF: 0.0811

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

GnomAD4 genome AF: 0.0887 AC: 13493 AN: 152088 Hom.: 1209 Cov.: 32 AF XY: 0.0887 AC XY: 6595 AN XY: 74360

African (AFR) AF: 0.235 AC: 9756 AN: 41466

American (AMR) AF: 0.0480 AC: 733 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0355 AC: 123 AN: 3468

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5166

South Asian (SAS) AF: 0.0474 AC: 229 AN: 4830

European-Finnish (FIN) AF: 0.0631 AC: 669 AN: 10610

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0252 AC: 1711 AN: 67976

Other (OTH) AF: 0.0812 AC: 171 AN: 2106

Alfa AF: 0.0655 Hom.: 97

Bravo AF: 0.0944

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.4
DANN	Benign	0.80
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1946380; hg19: chr8-86987363;