ENST00000626400.2:n.-215T>C

Variant names:

• chr11-129591276-T-C
• rs11820646
• ENST00000626400.2:n.-215T>C

Variant summary

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

The ENST00000626400.2(ENSG00000281386):​n.-215T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,964 control chromosomes in the GnomAD database, including 32,114 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 0.64 (32114 hom., cov: 31)
• Consequence: ENSG00000281386 ENST00000626400.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 67 publications found

Genes affected

ENSG00000281386 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000281386	ENST00000626400.2	n.-215T>C		upstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97708 AN: 151846 Hom.: 32078 Cov.: 31

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.644 AC: 97801 AN: 151964 Hom.: 32114 Cov.: 31 AF XY: 0.640 AC XY: 47513 AN XY: 74252

African (AFR) AF: 0.772 AC: 32006 AN: 41458

American (AMR) AF: 0.596 AC: 9100 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2232 AN: 3468

East Asian (EAS) AF: 0.534 AC: 2747 AN: 5140

South Asian (SAS) AF: 0.687 AC: 3296 AN: 4800

European-Finnish (FIN) AF: 0.518 AC: 5471 AN: 10556

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40814 AN: 67956

Other (OTH) AF: 0.653 AC: 1379 AN: 2112

Alfa AF: 0.616 Hom.: 54821

Bravo AF: 0.650

Asia WGS AF: 0.643 AC: 2233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.83
DANN	Benign	0.64
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs11820646; hg19: chr11-129461171;