11-69346225-G-T

Variant names:

• chr11-69346225-G-T
• rs4584599
• ENST00000540356.1:n.123+4547G>T

Variant summary

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

The ENST00000540356.1(ENSG00000260877):​n.123+4547G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,134 control chromosomes in the GnomAD database, including 2,780 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 0.15 (2780 hom., cov: 32)
• Consequence: ENSG00000260877 ENST00000540356.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 2 publications found

Genes affected

ENSG00000260877 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000540356.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260877	ENST00000540356.1	TSL:3	n.123+4547G>T		intron	N/A
	ENSG00000260877	ENST00000541137.5	TSL:3	n.246+4547G>T		intron	N/A
	ENSG00000260877	ENST00000544781.5	TSL:2	n.324+4547G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23249 AN: 152016 Hom.: 2764 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0498

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0594

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.153 AC: 23314 AN: 152134 Hom.: 2780 Cov.: 32 AF XY: 0.154 AC XY: 11425 AN XY: 74386

African (AFR) AF: 0.305 AC: 12619 AN: 41438

American (AMR) AF: 0.219 AC: 3349 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3472

East Asian (EAS) AF: 0.314 AC: 1621 AN: 5166

South Asian (SAS) AF: 0.113 AC: 547 AN: 4824

European-Finnish (FIN) AF: 0.0498 AC: 528 AN: 10604

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0594 AC: 4037 AN: 68016

Other (OTH) AF: 0.144 AC: 305 AN: 2114

Alfa AF: 0.0852 Hom.: 1643

Bravo AF: 0.175

Asia WGS AF: 0.204 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.34
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs4584599; hg19: chr11-69160993;