rs2067591

Variant names:

• chr11-32167193-T-C
• rs2067591

Variant summary

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

The variant allele was found at a frequency of 0.138 in 152,192 control chromosomes in the GnomAD database, including 1,641 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 (1641 hom., cov: 32)
• Consequence: THEM7P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 1 publications found

Genes affected

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

ENSG00000255252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THEM7P		n.32167193T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THEM7P	ENST00000419556.2	n.293-54765A>G		intron_variant	Intron 2 of 2	6
ENSG00000255252	ENST00000757560.1	n.138+6265A>G		intron_variant	Intron 1 of 6
ENSG00000255252	ENST00000757561.1	n.93+6265A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20921 AN: 152072 Hom.: 1640 Cov.: 32

Gnomad AFR AF: 0.0593

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.138 AC: 20940 AN: 152192 Hom.: 1641 Cov.: 32 AF XY: 0.141 AC XY: 10498 AN XY: 74396

African (AFR) AF: 0.0591 AC: 2455 AN: 41534

American (AMR) AF: 0.141 AC: 2161 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1382 AN: 5168

South Asian (SAS) AF: 0.200 AC: 964 AN: 4822

European-Finnish (FIN) AF: 0.217 AC: 2293 AN: 10590

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10797 AN: 68000

Other (OTH) AF: 0.145 AC: 306 AN: 2112

Alfa AF: 0.139 Hom.: 194

Bravo AF: 0.130

Asia WGS AF: 0.279 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.061
DANN	Benign	0.34
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2067591; hg19: chr11-32188739;