rs6785385

Variant names:

• chr3-81940699-A-G
• rs6785385
• ENST00000654999.1:n.1138+1758A>G

Variant summary

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

The ENST00000654999.1(ENSG00000242009):​n.1138+1758A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,784 control chromosomes in the GnomAD database, including 23,164 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 0.53 (23164 hom., cov: 31)
• Consequence: ENSG00000242009 ENST00000654999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.513
• Publications: 3 publications found

Genes affected

ENSG00000242009 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654999.1. 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
	ENSG00000242009	ENST00000654999.1		n.1138+1758A>G		intron	N/A
	ENSG00000242009	ENST00000670278.1		n.1291+1758A>G		intron	N/A
	ENSG00000242009	ENST00000768698.1		n.240+1758A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.534 AC: 80925 AN: 151666 Hom.: 23142 Cov.: 31

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.534 AC: 80999 AN: 151784 Hom.: 23164 Cov.: 31 AF XY: 0.533 AC XY: 39526 AN XY: 74180

African (AFR) AF: 0.728 AC: 30175 AN: 41450

American (AMR) AF: 0.496 AC: 7558 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1045 AN: 3470

East Asian (EAS) AF: 0.823 AC: 4237 AN: 5150

South Asian (SAS) AF: 0.358 AC: 1720 AN: 4808

European-Finnish (FIN) AF: 0.476 AC: 5023 AN: 10550

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29714 AN: 67796

Other (OTH) AF: 0.492 AC: 1036 AN: 2104

Alfa AF: 0.504 Hom.: 2633

Bravo AF: 0.551

Asia WGS AF: 0.588 AC: 2044 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.44
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs6785385; hg19: chr3-81989850;