rs2672794

Variant names:

• chr11-1219775-T-C
• rs2672794
• ENST00000654177.1:n.660-215T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654177.1(ENSG00000286275):​n.660-215T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 151,910 control chromosomes in the GnomAD database, including 37,581 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 0.69 (37581 hom., cov: 31)
• Consequence: ENSG00000286275 ENST00000654177.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

ENSG00000286275 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 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
ENSG00000286275	ENST00000654177.1	n.660-215T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104804 AN: 151792 Hom.: 37518 Cov.: 31

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.691 AC: 104931 AN: 151910 Hom.: 37581 Cov.: 31 AF XY: 0.689 AC XY: 51168 AN XY: 74240

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.684

Alfa AF: 0.640 Hom.: 27283

Bravo AF: 0.707

Asia WGS AF: 0.589 AC: 2048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2672794; hg19: chr11-1241005;