11-20247844-A-G

Variant names:

• chr11-20247844-A-G
• rs1520896
• ENST00000725917.1:n.616+23939A>G

Variant summary

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

The ENST00000725917.1(ENSG00000294773):​n.616+23939A>G variant causes a intron change. The variant allele was found at a frequency of 0.765 in 152,088 control chromosomes in the GnomAD database, including 45,179 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 0.76 (45179 hom., cov: 32)
• Consequence: ENSG00000294773 ENST00000725917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.72
• Publications: 7 publications found

Genes affected

ENSG00000294773 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725917.1. 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
	ENSG00000294773	ENST00000725917.1		n.616+23939A>G		intron	N/A
	ENSG00000294773	ENST00000725918.1		n.179-26541A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116236 AN: 151970 Hom.: 45148 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.765 AC: 116317 AN: 152088 Hom.: 45179 Cov.: 32 AF XY: 0.768 AC XY: 57066 AN XY: 74346

African (AFR) AF: 0.639 AC: 26472 AN: 41446

American (AMR) AF: 0.750 AC: 11455 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2730 AN: 3472

East Asian (EAS) AF: 0.646 AC: 3340 AN: 5170

South Asian (SAS) AF: 0.915 AC: 4401 AN: 4810

European-Finnish (FIN) AF: 0.818 AC: 8677 AN: 10604

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56588 AN: 68002

Other (OTH) AF: 0.764 AC: 1613 AN: 2110

Alfa AF: 0.803 Hom.: 183501

Bravo AF: 0.749

Asia WGS AF: 0.780 AC: 2717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	19
DANN	Benign	0.70
PhyloP100		4.7

Splicing

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

Other links and lift over

dbSNP: rs1520896; hg19: chr11-20269390;