rs10893679

Variant names:

• chr11-127411484-G-A
• rs10893679
• ENST00000822754.1:n.106-16357G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-127411484-G-A
• chr11-127411484-G-C

Variant summary

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

The ENST00000822754.1(ENSG00000307024):​n.106-16357G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,212 control chromosomes in the GnomAD database, including 1,665 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 0.14 (1665 hom., cov: 33)
• Consequence: ENSG00000307024 ENST00000822754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359
• Publications: 1 publications found

Genes affected

ENSG00000307024 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822754.1. 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
	ENSG00000307024	ENST00000822754.1		n.106-16357G>A		intron	N/A
	ENSG00000307024	ENST00000822755.1		n.143-16357G>A		intron	N/A
	ENSG00000307024	ENST00000822756.1		n.97-16357G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20849 AN: 152094 Hom.: 1661 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0904

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.137 AC: 20859 AN: 152212 Hom.: 1665 Cov.: 33 AF XY: 0.138 AC XY: 10297 AN XY: 74424

African (AFR) AF: 0.204 AC: 8479 AN: 41526

American (AMR) AF: 0.0905 AC: 1383 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 507 AN: 3470

East Asian (EAS) AF: 0.166 AC: 860 AN: 5170

South Asian (SAS) AF: 0.256 AC: 1233 AN: 4824

European-Finnish (FIN) AF: 0.102 AC: 1081 AN: 10598

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6932 AN: 68014

Other (OTH) AF: 0.146 AC: 308 AN: 2114

Alfa AF: 0.0366 Hom.: 38

Bravo AF: 0.137

Asia WGS AF: 0.234 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.46
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10893679; hg19: chr11-127281379;