rs1286005

Variant names:

• chr6-7046219-T-C
• rs1286005
• ENST00000840662.1:n.111-3245A>G

Variant summary

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

The ENST00000840662.1(ENSG00000309384):​n.111-3245A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,798 control chromosomes in the GnomAD database, including 22,390 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 0.51 (22390 hom., cov: 30)
• Consequence: ENSG00000309384 ENST00000840662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.979
• Publications: 4 publications found

Genes affected

ENSG00000309384 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309384	ENST00000840662.1	n.111-3245A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76963 AN: 151680 Hom.: 22387 Cov.: 30

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.0670

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.507 AC: 76993 AN: 151798 Hom.: 22390 Cov.: 30 AF XY: 0.502 AC XY: 37265 AN XY: 74162

African (AFR) AF: 0.272 AC: 11234 AN: 41360

American (AMR) AF: 0.526 AC: 8004 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2150 AN: 3472

East Asian (EAS) AF: 0.0677 AC: 350 AN: 5168

South Asian (SAS) AF: 0.346 AC: 1662 AN: 4810

European-Finnish (FIN) AF: 0.623 AC: 6553 AN: 10520

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45040 AN: 67948

Other (OTH) AF: 0.552 AC: 1161 AN: 2104

Alfa AF: 0.611 Hom.: 49041

Bravo AF: 0.488

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.7
DANN	Benign	0.66
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs1286005; hg19: chr6-7046452;