11-34434394-T-C

Variant names:

• chr11-34434394-T-C
• rs208682
• ENST00000724590.1:n.206+1277T>C

Variant summary

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

The ENST00000724590.1(ENSG00000294594):​n.206+1277T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,244 control chromosomes in the GnomAD database, including 54,948 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 0.85 (54948 hom., cov: 32)
• Consequence: ENSG00000294594 ENST00000724590.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• Publications: 15 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376622	XR_931180.3	n.265+1277T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294594	ENST00000724590.1	n.206+1277T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128810 AN: 152126 Hom.: 54897 Cov.: 32

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.847 AC: 128912 AN: 152244 Hom.: 54948 Cov.: 32 AF XY: 0.842 AC XY: 62692 AN XY: 74432

African (AFR) AF: 0.943 AC: 39194 AN: 41550

American (AMR) AF: 0.757 AC: 11567 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3010 AN: 3470

East Asian (EAS) AF: 0.816 AC: 4219 AN: 5172

South Asian (SAS) AF: 0.803 AC: 3874 AN: 4826

European-Finnish (FIN) AF: 0.793 AC: 8408 AN: 10600

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56039 AN: 68022

Other (OTH) AF: 0.830 AC: 1754 AN: 2114

Alfa AF: 0.830 Hom.: 75010

Bravo AF: 0.847

Asia WGS AF: 0.808 AC: 2810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs208682; hg19: chr11-34455941;