rs4244480

Positions:

• chr11-32194697-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+35423A>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 0.536 in 152,072 control chromosomes in the GnomAD database, including 23,797 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 0.54 (23797 hom., cov: 32)
• Consequence: THEM7P ENST00000419556.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
THEM7P	ENST00000419556.2	n.292+35423A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81376 AN: 151956 Hom.: 23756 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.536 AC: 81481 AN: 152072 Hom.: 23797 Cov.: 32 AF XY: 0.535 AC XY: 39781 AN XY: 74336

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.538

Alfa AF: 0.481 Hom.: 2485

Bravo AF: 0.546

Asia WGS AF: 0.593 AC: 2061 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4244480; hg19: chr11-32216243;