11-91269441-G-C

Variant names:

• chr11-91269441-G-C
• rs10830693
• ENST00000733467.1:n.-219G>C

Variant summary

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

The ENST00000733467.1(ENSG00000295883):​n.-219G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,806 control chromosomes in the GnomAD database, including 4,695 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 0.23 (4695 hom., cov: 30)
• Consequence: ENSG00000295883 ENST00000733467.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 2 publications found

Genes affected

ENSG00000295883 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 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
ENSG00000295883	ENST00000733467.1	n.-219G>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34203 AN: 151690 Hom.: 4673 Cov.: 30

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.226 AC: 34275 AN: 151806 Hom.: 4695 Cov.: 30 AF XY: 0.228 AC XY: 16892 AN XY: 74180

African (AFR) AF: 0.376 AC: 15534 AN: 41364

American (AMR) AF: 0.213 AC: 3257 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3468

East Asian (EAS) AF: 0.380 AC: 1937 AN: 5100

South Asian (SAS) AF: 0.127 AC: 609 AN: 4800

European-Finnish (FIN) AF: 0.213 AC: 2245 AN: 10542

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9735 AN: 67944

Other (OTH) AF: 0.240 AC: 506 AN: 2106

Alfa AF: 0.0828 Hom.: 106

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.75
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs10830693; hg19: chr11-91002609;