ENST00000839775.1:n.78-2627T>C

Variant names:

• chr11-30738788-T-C
• rs3925584
• ENST00000839775.1:n.78-2627T>C

Variant summary

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

The ENST00000839775.1(ENSG00000309240):​n.78-2627T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,964 control chromosomes in the GnomAD database, including 11,162 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 0.35 (11162 hom., cov: 31)
• Consequence: ENSG00000309240 ENST00000839775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 43 publications found

Genes affected

ENSG00000309240 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928338	XR_007062640.1	n.78-2627T>C		intron_variant	Intron 1 of 4
LOC101928338	XR_242862.5	n.78-2627T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309240	ENST00000839775.1	n.78-2627T>C		intron_variant	Intron 1 of 4
ENSG00000309240	ENST00000839776.1	n.49-2627T>C		intron_variant	Intron 1 of 5
ENSG00000309240	ENST00000839777.1	n.49-2627T>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53514 AN: 151846 Hom.: 11166 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.352 AC: 53509 AN: 151964 Hom.: 11162 Cov.: 31 AF XY: 0.353 AC XY: 26213 AN XY: 74264

African (AFR) AF: 0.123 AC: 5118 AN: 41514

American (AMR) AF: 0.429 AC: 6539 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1606 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1787 AN: 5098

South Asian (SAS) AF: 0.273 AC: 1316 AN: 4814

European-Finnish (FIN) AF: 0.485 AC: 5124 AN: 10566

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30832 AN: 67936

Other (OTH) AF: 0.380 AC: 802 AN: 2108

Alfa AF: 0.424 Hom.: 60316

Bravo AF: 0.340

Asia WGS AF: 0.321 AC: 1117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.56
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs3925584; hg19: chr11-30760335;