ENST00000777942.1:n.70+6859A>C

Variant names:

• chr3-66965486-T-G
• rs6807497
• ENST00000777942.1:n.70+6859A>C

Variant summary

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

The ENST00000777942.1(ENSG00000288039):​n.70+6859A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,080 control chromosomes in the GnomAD database, including 46,660 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 0.78 (46660 hom., cov: 31)
• Consequence: ENSG00000288039 ENST00000777942.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 1 publications found

Genes affected

ENSG00000288039 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777942.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288039	ENST00000777942.1		n.70+6859A>C		intron	N/A
	ENSG00000288039	ENST00000777943.1		n.65+6859A>C		intron	N/A
	ENSG00000288039	ENST00000777944.1		n.46+6859A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118666 AN: 151962 Hom.: 46614 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.781 AC: 118771 AN: 152080 Hom.: 46660 Cov.: 31 AF XY: 0.785 AC XY: 58332 AN XY: 74334

African (AFR) AF: 0.711 AC: 29485 AN: 41458

American (AMR) AF: 0.826 AC: 12629 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2457 AN: 3472

East Asian (EAS) AF: 0.964 AC: 4972 AN: 5160

South Asian (SAS) AF: 0.929 AC: 4482 AN: 4822

European-Finnish (FIN) AF: 0.782 AC: 8266 AN: 10566

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53960 AN: 67996

Other (OTH) AF: 0.771 AC: 1631 AN: 2116

Alfa AF: 0.788 Hom.: 75300

Bravo AF: 0.778

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.51
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs6807497; hg19: chr3-67015910;