rs4766921

Variant names:

• chr12-118913063-G-A
• rs4766921
• ENST00000726771.1:n.449-7135G>A

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000726771.1(ENSG00000294918):​n.449-7135G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,108 control chromosomes in the GnomAD database, including 5,463 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 0.26 (5463 hom., cov: 32)
• Consequence: ENSG00000294918 ENST00000726771.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.15
• Publications: 4 publications found

Genes affected

ENSG00000294918 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370019	XR_945423.3	n.444-7135G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294918	ENST00000726771.1	n.449-7135G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39397 AN: 151990 Hom.: 5465 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.259 AC: 39405 AN: 152108 Hom.: 5463 Cov.: 32 AF XY: 0.255 AC XY: 18928 AN XY: 74356

African (AFR) AF: 0.162 AC: 6726 AN: 41486

American (AMR) AF: 0.275 AC: 4211 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1288 AN: 3470

East Asian (EAS) AF: 0.161 AC: 830 AN: 5170

South Asian (SAS) AF: 0.158 AC: 762 AN: 4824

European-Finnish (FIN) AF: 0.317 AC: 3352 AN: 10576

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21329 AN: 67974

Other (OTH) AF: 0.263 AC: 555 AN: 2112

Alfa AF: 0.302 Hom.: 9449

Bravo AF: 0.259

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	16
DANN	Benign	0.80
PhyloP100		3.2

Splicing

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

Other links and lift over

dbSNP: rs4766921; hg19: chr12-119350868;