rs7944342

Variant names:

• chr11-32266398-T-C
• rs7944342
• ENST00000525689.2:n.123-36037A>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000525689.2(THEM7P):​n.123-36037A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,108 control chromosomes in the GnomAD database, including 3,443 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 0.20 (3443 hom., cov: 32)
• Consequence: THEM7P ENST00000525689.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.51

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 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	ENST00000525689.2	n.123-36037A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29906 AN: 151990 Hom.: 3441 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.197 AC: 29909 AN: 152108 Hom.: 3443 Cov.: 32 AF XY: 0.196 AC XY: 14610 AN XY: 74390

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.0213

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.213

Alfa AF: 0.230 Hom.: 2123

Bravo AF: 0.188

Asia WGS AF: 0.0720 AC: 249 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	16
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7944342; hg19: chr11-32287944;