2-144747126-T-G

Position:

• chr2-144747126-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000445791.5(TEX41):​n.125-20972T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,250 control chromosomes in the GnomAD database, including 1,003 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 0.10 (1003 hom., cov: 32)
• Consequence: TEX41 ENST00000445791.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461

Genes affected

TEX41 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX41	NR_033870.2	n.143-20972T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX41	ENST00000445791.5	n.125-20972T>G		intron_variant		1
TEX41	ENST00000451774.5	n.84-20972T>G		intron_variant		1
TEX41	ENST00000414256.5	n.154-20972T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15593 AN: 152132 Hom.: 994 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0469

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.0821

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.103 AC: 15636 AN: 152250 Hom.: 1003 Cov.: 32 AF XY: 0.0998 AC XY: 7433 AN XY: 74454

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0469

Gnomad4 ASJ AF: 0.0726

Gnomad4 EAS AF: 0.00328

Gnomad4 SAS AF: 0.0435

Gnomad4 FIN AF: 0.0821

Gnomad4 NFE AF: 0.0869

Gnomad4 OTH AF: 0.0842

Alfa AF: 0.0849 Hom.: 1260

Bravo AF: 0.105

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7603516; hg19: chr2-145504693;