chr3-66965486-T-G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377144	XR_940939.2	n.74+6859A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288039	ENST00000777942.1	n.70+6859A>C		intron_variant	Intron 1 of 3
ENSG00000288039	ENST00000777943.1	n.65+6859A>C		intron_variant	Intron 1 of 3
ENSG00000288039	ENST00000777944.1	n.46+6859A>C		intron_variant	Intron 1 of 4
ENSG00000288039	ENST00000777946.1	n.70+6859A>C		intron_variant	Intron 1 of 2

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 v4.3

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;