rs1946380

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656790.1. 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
	ENSG00000287927	ENST00000656790.1		n.729A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000287927	ENST00000751425.1		n.814A>G		non_coding_transcript_exon	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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1946380;

hg19: chr8-86987363;