rs12577592

Variant names:

• chr11-32186915-T-C
• rs12577592
• ENST00000419556.2:n.292+43205A>G

Variant summary

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

The ENST00000419556.2(THEM7P):​n.292+43205A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,186 control chromosomes in the GnomAD database, including 1,721 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 0.14 (1721 hom., cov: 32)
• Consequence: THEM7P ENST00000419556.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.50

Genes affected

THEM7P (HGNC:50386): (thioesterase superfamily member 7, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.194 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
THEM7P	ENST00000419556.2	n.292+43205A>G		intron_variant	Intron 2 of 2	6

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21481 AN: 152066 Hom.: 1721 Cov.: 32

Gnomad AFR AF: 0.0526

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.176

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.141 AC: 21484 AN: 152186 Hom.: 1721 Cov.: 32 AF XY: 0.144 AC XY: 10727 AN XY: 74400

Gnomad4 AFR AF: 0.0525

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.151

Alfa AF: 0.162 Hom.: 434

Bravo AF: 0.134

Asia WGS AF: 0.183 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12577592; hg19: chr11-32208461;