rs12280753

Variant names:

• chr11-116742944-C-T
• rs12280753
• ENST00000836679.1:n.433+4430C>T

Variant summary

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

The ENST00000836679.1(ENSG00000308823):​n.433+4430C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,114 control chromosomes in the GnomAD database, including 1,912 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 0.13 (1912 hom., cov: 32)
• Consequence: ENSG00000308823 ENST00000836679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 25 publications found

Genes affected

ENSG00000308823 (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 = 0.26 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
ENSG00000308823	ENST00000836679.1	n.433+4430C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19833 AN: 151996 Hom.: 1903 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0902

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.0607

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0744

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.131 AC: 19876 AN: 152114 Hom.: 1912 Cov.: 32 AF XY: 0.129 AC XY: 9592 AN XY: 74382

African (AFR) AF: 0.264 AC: 10928 AN: 41444

American (AMR) AF: 0.147 AC: 2252 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0902 AC: 313 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0496 AC: 239 AN: 4822

European-Finnish (FIN) AF: 0.0607 AC: 643 AN: 10590

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0744 AC: 5062 AN: 67998

Other (OTH) AF: 0.133 AC: 282 AN: 2114

Alfa AF: 0.0977 Hom.: 1908

Bravo AF: 0.143

Asia WGS AF: 0.0460 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.57
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs12280753; hg19: chr11-116613660;