rs11045777

Variant names:

• chr12-21126647-G-A
• rs11045777
• ENST00000593147.5:n.*114+390G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-21126647-G-A
• chr12-21126647-G-T

Variant summary

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

The ENST00000593147.5(ENSG00000257062):​n.*114+390G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 151,978 control chromosomes in the GnomAD database, including 2,066 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 0.15 (2066 hom., cov: 31)
• Consequence: ENSG00000257062 ENST00000593147.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

Genes affected

ENSG00000257062 (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 = 0.192 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
ENSG00000257062	ENST00000593147.5	n.*114+390G>A		intron_variant	Intron 5 of 5	5		ENSP00000467209.1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23371 AN: 151860 Hom.: 2067 Cov.: 31

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0715

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.154 AC: 23373 AN: 151978 Hom.: 2066 Cov.: 31 AF XY: 0.146 AC XY: 10874 AN XY: 74288

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0718

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.165

Alfa AF: 0.192 Hom.: 2900

Bravo AF: 0.158

Asia WGS AF: 0.0400 AC: 140 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	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11045777; hg19: chr12-21279581; COSMIC: COSV57016556;