rs12577592

Positions:

• chr11-32186915-T-C

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THEM7P	ENST00000419556.2	n.292+43205A>G		intron_variant, non_coding_transcript_variant

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;