chr11-30736617-T-G

Variant names:

• chr11-30736617-T-G
• rs628029
• ENST00000839775.1:n.78-4798T>G

Variant summary

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

The ENST00000839775.1(ENSG00000309240):​n.78-4798T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,870 control chromosomes in the GnomAD database, including 12,330 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 0.40 (12330 hom., cov: 31)
• Consequence: ENSG00000309240 ENST00000839775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.519 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.78-4798T>G		intron	N/A
	ENSG00000309240	ENST00000839776.1		n.49-4798T>G		intron	N/A
	ENSG00000309240	ENST00000839777.1		n.49-4798T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60431 AN: 151754 Hom.: 12313 Cov.: 31

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.398 AC: 60490 AN: 151870 Hom.: 12330 Cov.: 31 AF XY: 0.398 AC XY: 29513 AN XY: 74186

African (AFR) AF: 0.341 AC: 14113 AN: 41432

American (AMR) AF: 0.348 AC: 5294 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1215 AN: 3464

East Asian (EAS) AF: 0.486 AC: 2495 AN: 5130

South Asian (SAS) AF: 0.537 AC: 2582 AN: 4812

European-Finnish (FIN) AF: 0.390 AC: 4114 AN: 10538

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29325 AN: 67956

Other (OTH) AF: 0.382 AC: 805 AN: 2108

Alfa AF: 0.315 Hom.: 1201

Bravo AF: 0.392

Asia WGS AF: 0.464 AC: 1614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.42
DANN	Benign	0.49
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs628029; hg19: chr11-30758164;