11-30738788-T-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: 44 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839775.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309240	ENST00000839775.1		n.78-2627T>C		intron	N/A
	ENSG00000309240	ENST00000839776.1		n.49-2627T>C		intron	N/A
	ENSG00000309240	ENST00000839777.1		n.49-2627T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3925584;

hg19: chr11-30760335;