12-77158363-A-G

Variant names:

• chr12-77158363-A-G
• rs1175593
• ENST00000667988.1:n.43-4570A>G

Variant summary

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

The ENST00000667988.1(ENSG00000286476):​n.43-4570A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,796 control chromosomes in the GnomAD database, including 4,835 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 0.22 (4835 hom., cov: 33)
• Consequence: ENSG00000286476 ENST00000667988.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 1 publications found

Genes affected

ENSG00000286476 (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 (EAS) allele frequency at 95% confidence interval = 0.493 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
ENSG00000286476	ENST00000667988.1	n.43-4570A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33984 AN: 151678 Hom.: 4825 Cov.: 33

Gnomad AFR AF: 0.0561

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.224 AC: 34009 AN: 151796 Hom.: 4835 Cov.: 33 AF XY: 0.232 AC XY: 17214 AN XY: 74164

African (AFR) AF: 0.0561 AC: 2329 AN: 41496

American (AMR) AF: 0.329 AC: 5002 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 945 AN: 3468

East Asian (EAS) AF: 0.509 AC: 2629 AN: 5166

South Asian (SAS) AF: 0.339 AC: 1632 AN: 4820

European-Finnish (FIN) AF: 0.283 AC: 2986 AN: 10550

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17600 AN: 67800

Other (OTH) AF: 0.233 AC: 491 AN: 2106

Alfa AF: 0.250 Hom.: 7599

Bravo AF: 0.219

Asia WGS AF: 0.382 AC: 1327 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.35
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1175593; hg19: chr12-77552143;