ENST00000707189.1:n.1000-75636G>A

Variant names:

• chr6-26477551-G-A
• rs6456728
• ENST00000707189.1:n.1000-75636G>A

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.1000-75636G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 149,426 control chromosomes in the GnomAD database, including 9,466 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 0.30 (9466 hom., cov: 31)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 19 publications found

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC285819	NR_038992.1	n.1325-70C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291336	ENST00000707189.1	n.1000-75636G>A		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1001-55154G>A		intron_variant	Intron 1 of 1
ENSG00000300236	ENST00000770281.1	n.559-5358C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45304 AN: 149326 Hom.: 9438 Cov.: 31

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.304 AC: 45375 AN: 149426 Hom.: 9466 Cov.: 31 AF XY: 0.296 AC XY: 21596 AN XY: 72840

African (AFR) AF: 0.606 AC: 24838 AN: 41016

American (AMR) AF: 0.212 AC: 3181 AN: 15026

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 566 AN: 3430

East Asian (EAS) AF: 0.164 AC: 835 AN: 5102

South Asian (SAS) AF: 0.229 AC: 1086 AN: 4742

European-Finnish (FIN) AF: 0.134 AC: 1322 AN: 9882

Middle Eastern (MID) AF: 0.231 AC: 67 AN: 290

European-Non Finnish (NFE) AF: 0.189 AC: 12685 AN: 66972

Other (OTH) AF: 0.280 AC: 578 AN: 2064

Alfa AF: 0.243 Hom.: 9803

Bravo AF: 0.321

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.31
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs6456728; hg19: chr6-26477779;