rs4244480

Variant names:

• chr11-32194697-T-C
• rs4244480
• ENST00000419556.2:n.292+35423A>G

Variant summary

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

The ENST00000419556.2(THEM7P):​n.292+35423A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THEM7P	ENST00000419556.2	n.292+35423A>G		intron_variant	Intron 2 of 2	6

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

African (AFR) AF: 0.789 AC: 32739 AN: 41498

American (AMR) AF: 0.453 AC: 6922 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1825 AN: 3470

East Asian (EAS) AF: 0.491 AC: 2528 AN: 5152

South Asian (SAS) AF: 0.562 AC: 2707 AN: 4816

European-Finnish (FIN) AF: 0.417 AC: 4404 AN: 10560

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.423 AC: 28734 AN: 67986

Other (OTH) AF: 0.538 AC: 1138 AN: 2116

Alfa AF: 0.474 Hom.: 26451

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
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs4244480; hg19: chr11-32216243;