rs11045773

Variant names:

• chr12-21119368-A-G
• rs11045773
• ENST00000593147.5:n.256-6740A>G

Variant summary

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

The ENST00000593147.5(ENSG00000257062):​n.256-6740A>G 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 152,156 control chromosomes in the GnomAD database, including 1,806 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 (1806 hom., cov: 32)
• Consequence: ENSG00000257062 ENST00000593147.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 7 publications found

Genes affected

ENSG00000257062 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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.256-6740A>G		intron_variant	Intron 4 of 5	5		ENSP00000467209.1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20006 AN: 152038 Hom.: 1808 Cov.: 32

Gnomad AFR AF: 0.0364

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.131 AC: 19994 AN: 152156 Hom.: 1806 Cov.: 32 AF XY: 0.125 AC XY: 9322 AN XY: 74390

African (AFR) AF: 0.0364 AC: 1511 AN: 41526

American (AMR) AF: 0.139 AC: 2120 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 887 AN: 3470

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5176

South Asian (SAS) AF: 0.0716 AC: 346 AN: 4830

European-Finnish (FIN) AF: 0.104 AC: 1103 AN: 10592

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13221 AN: 67976

Other (OTH) AF: 0.148 AC: 313 AN: 2112

Alfa AF: 0.161 Hom.: 1752

Bravo AF: 0.133

Asia WGS AF: 0.0330 AC: 115 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.48
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs11045773; hg19: chr12-21272302;