rs12275055

Variant names:

• chr11-69213892-A-G
• rs12275055
• ENST00000779509.1:n.138+17710A>G

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.138+17710A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,232 control chromosomes in the GnomAD database, including 1,298 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 0.12 (1298 hom., cov: 32)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 13 publications found

Genes affected

ENSG00000301530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 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
ENSG00000301530	ENST00000779509.1	n.138+17710A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18106 AN: 152114 Hom.: 1299 Cov.: 32

Gnomad AFR AF: 0.0591

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.0777

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.119 AC: 18099 AN: 152232 Hom.: 1298 Cov.: 32 AF XY: 0.115 AC XY: 8577 AN XY: 74442

African (AFR) AF: 0.0589 AC: 2448 AN: 41540

American (AMR) AF: 0.107 AC: 1640 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 824 AN: 3470

East Asian (EAS) AF: 0.0147 AC: 76 AN: 5184

South Asian (SAS) AF: 0.0782 AC: 377 AN: 4824

European-Finnish (FIN) AF: 0.0836 AC: 887 AN: 10614

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11367 AN: 67984

Other (OTH) AF: 0.151 AC: 319 AN: 2114

Alfa AF: 0.156 Hom.: 875

Bravo AF: 0.120

Asia WGS AF: 0.0560 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.74
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs12275055; hg19: chr11-68981359;