11-106198621-C-T

Variant names:

• chr11-106198621-C-T
• rs1893854
• ENST00000727604.1:n.276+21291C>T

Variant summary

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

The ENST00000727604.1(ENSG00000295041):​n.276+21291C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 151,980 control chromosomes in the GnomAD database, including 34,444 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 0.63 (34444 hom., cov: 31)
• Consequence: ENSG00000295041 ENST00000727604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 1 publications found

Genes affected

ENSG00000295041 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727604.1. 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
	ENSG00000295041	ENST00000727604.1		n.276+21291C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95671 AN: 151862 Hom.: 34441 Cov.: 31

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.630 AC: 95676 AN: 151980 Hom.: 34444 Cov.: 31 AF XY: 0.632 AC XY: 46924 AN XY: 74254

African (AFR) AF: 0.254 AC: 10537 AN: 41426

American (AMR) AF: 0.704 AC: 10733 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2472 AN: 3470

East Asian (EAS) AF: 0.637 AC: 3284 AN: 5156

South Asian (SAS) AF: 0.692 AC: 3335 AN: 4816

European-Finnish (FIN) AF: 0.789 AC: 8354 AN: 10584

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.805 AC: 54727 AN: 67976

Other (OTH) AF: 0.635 AC: 1340 AN: 2110

Alfa AF: 0.690 Hom.: 6311

Bravo AF: 0.607

Asia WGS AF: 0.613 AC: 2135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.37
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1893854; hg19: chr11-106069348;