11-62930341-G-T

Variant names:

• chr11-62930341-G-T
• rs4592425
• ENST00000782248.1:n.429G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000782248.1(ENSG00000301851):​n.429G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,122 control chromosomes in the GnomAD database, including 47,429 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 0.78 (47429 hom., cov: 31)
• Consequence: ENSG00000301851 ENST00000782248.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715
• Publications: 6 publications found

Genes affected

ENSG00000301851 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782248.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301851	ENST00000782248.1		n.429G>T		non_coding_transcript_exon	Exon 3 of 6
	ENSG00000301851	ENST00000782249.1		n.502G>T		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119080 AN: 152004 Hom.: 47369 Cov.: 31

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.784 AC: 119197 AN: 152122 Hom.: 47429 Cov.: 31 AF XY: 0.788 AC XY: 58562 AN XY: 74354

African (AFR) AF: 0.929 AC: 38560 AN: 41528

American (AMR) AF: 0.784 AC: 11986 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2617 AN: 3470

East Asian (EAS) AF: 0.883 AC: 4556 AN: 5162

South Asian (SAS) AF: 0.808 AC: 3890 AN: 4816

European-Finnish (FIN) AF: 0.751 AC: 7944 AN: 10582

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.694 AC: 47136 AN: 67964

Other (OTH) AF: 0.761 AC: 1606 AN: 2110

Alfa AF: 0.720 Hom.: 47827

Bravo AF: 0.792

Asia WGS AF: 0.840 AC: 2920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	11
DANN	Benign	0.83
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs4592425; hg19: chr11-62697813;