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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376622	XR_931180.3	n.159+67A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294594	ENST00000724590.1	n.100+67A>G		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs208679; hg19: chr11-34454061;