rs2672794

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

ENSG00000286275 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654177.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286275	ENST00000654177.1		n.660-215T>C		intron	N/A

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

African (AFR) AF: 0.891 AC: 36918 AN: 41448

American (AMR) AF: 0.699 AC: 10683 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2105 AN: 3464

East Asian (EAS) AF: 0.384 AC: 1965 AN: 5114

South Asian (SAS) AF: 0.662 AC: 3191 AN: 4820

European-Finnish (FIN) AF: 0.585 AC: 6186 AN: 10566

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41649 AN: 67902

Other (OTH) AF: 0.684 AC: 1440 AN: 2106

Alfa AF: 0.649 Hom.: 79493

Bravo AF: 0.707

Asia WGS AF: 0.589 AC: 2048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.51
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2672794; hg19: chr11-1241005;