rs11104868

Variant names:

• chr12-88434665-G-A
• rs11104868
• ENST00000741490.1:n.*33G>A

Variant summary

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

The ENST00000741490.1(ENSG00000296741):​n.*33G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,114 control chromosomes in the GnomAD database, including 8,079 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 0.27 (8079 hom., cov: 33)
• Consequence: ENSG00000296741 ENST00000741490.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 9 publications found

Genes affected

ENSG00000296741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 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
ENSG00000296741	ENST00000741490.1	n.*33G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40841 AN: 151996 Hom.: 8039 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.269 AC: 40933 AN: 152114 Hom.: 8079 Cov.: 33 AF XY: 0.270 AC XY: 20059 AN XY: 74378

African (AFR) AF: 0.559 AC: 23175 AN: 41458

American (AMR) AF: 0.173 AC: 2648 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3470

East Asian (EAS) AF: 0.200 AC: 1034 AN: 5166

South Asian (SAS) AF: 0.255 AC: 1232 AN: 4822

European-Finnish (FIN) AF: 0.245 AC: 2590 AN: 10572

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9286 AN: 68008

Other (OTH) AF: 0.234 AC: 493 AN: 2110

Alfa AF: 0.177 Hom.: 11137

Bravo AF: 0.274

Asia WGS AF: 0.258 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs11104868; hg19: chr12-88828442;