rs208679

Variant names:

• chr11-34432514-A-G
• rs208679
• ENST00000724590.1:n.100+67A>G

Variant summary

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

The ENST00000724590.1(ENSG00000294594):​n.100+67A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0941 in 152,242 control chromosomes in the GnomAD database, including 862 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 0.094 (862 hom., cov: 32)
• Consequence: ENSG00000294594 ENST00000724590.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.612
• Publications: 12 publications found

Genes affected

ENSG00000294594 (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 (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724590.1. 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
	ENSG00000294594	ENST00000724590.1		n.100+67A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0940 AC: 14304 AN: 152124 Hom.: 856 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00441

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0941 AC: 14325 AN: 152242 Hom.: 862 Cov.: 32 AF XY: 0.0970 AC XY: 7219 AN XY: 74432

African (AFR) AF: 0.109 AC: 4520 AN: 41548

American (AMR) AF: 0.133 AC: 2030 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0685 AC: 238 AN: 3472

East Asian (EAS) AF: 0.232 AC: 1203 AN: 5178

South Asian (SAS) AF: 0.121 AC: 585 AN: 4822

European-Finnish (FIN) AF: 0.113 AC: 1198 AN: 10602

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0641 AC: 4358 AN: 68018

Other (OTH) AF: 0.0856 AC: 181 AN: 2114

Alfa AF: 0.0701 Hom.: 549

Bravo AF: 0.0963

Asia WGS AF: 0.182 AC: 631 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	3.2
DANN	Benign	0.67
PhyloP100		0.61

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: rs208679;

hg19: chr11-34454061;