chr2-144747126-T-G

Variant names:

• chr2-144747126-T-G
• rs7603516
• ENST00000445791.5:n.125-20972T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

TEX41 (HGNC:48667): (testis expressed 41)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445791.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX41	NR_033870.2		n.143-20972T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX41	ENST00000445791.5	TSL:1	n.125-20972T>G		intron	N/A
	TEX41	ENST00000451774.5	TSL:1	n.84-20972T>G		intron	N/A
	TEX41	ENST00000414256.5	TSL:5	n.154-20972T>G		intron	N/A

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

African (AFR) AF: 0.178 AC: 7380 AN: 41530

American (AMR) AF: 0.0469 AC: 718 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0726 AC: 252 AN: 3472

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5184

South Asian (SAS) AF: 0.0435 AC: 210 AN: 4826

European-Finnish (FIN) AF: 0.0821 AC: 872 AN: 10616

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0869 AC: 5910 AN: 68008

Other (OTH) AF: 0.0842 AC: 178 AN: 2114

Alfa AF: 0.0905 Hom.: 2236

Bravo AF: 0.105

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.46
PhyloP100		0.46
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7603516; hg19: chr2-145504693;