rs720333

Variant names:

• chr12-4384772-G-A
• rs720333
• ENST00000674624.1:n.*1204+18490G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-4384772-G-A
• chr12-4384772-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000674624.1(ENSG00000285901):​n.*1204+18490G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,066 control chromosomes in the GnomAD database, including 42,567 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 0.74 (42567 hom., cov: 32)
• Consequence: ENSG00000285901 ENST00000674624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

ENSG00000285901 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.845 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
ENSG00000285901	ENST00000674624.1	n.*1204+18490G>A		intron_variant	Intron 9 of 9			ENSP00000501898.1
ENSG00000285901	ENST00000648100.1	n.*1967+18490G>A		intron_variant	Intron 11 of 11			ENSP00000497536.1

Frequencies

GnomAD3 genomes AF: 0.737 AC: 112025 AN: 151946 Hom.: 42570 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.737 AC: 112046 AN: 152066 Hom.: 42567 Cov.: 32 AF XY: 0.732 AC XY: 54422 AN XY: 74332

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.750

Alfa AF: 0.819 Hom.: 30196

Bravo AF: 0.718

Asia WGS AF: 0.633 AC: 2202 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	1.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs720333; hg19: chr12-4493938;