2-144732530-A-G

Variant names:

• chr2-144732530-A-G
• rs900554
• ENST00000445791.5:n.125-35568A>G

Variant summary

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

The ENST00000445791.5(TEX41):​n.125-35568A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,046 control chromosomes in the GnomAD database, including 29,199 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 0.61 (29199 hom., cov: 31)
• Consequence: TEX41 ENST00000445791.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• 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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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.143-35568A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX41	ENST00000445791.5	TSL:1	n.125-35568A>G		intron	N/A
	TEX41	ENST00000451774.5	TSL:1	n.84-35568A>G		intron	N/A
	TEX41	ENST00000414256.5	TSL:5	n.154-35568A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.613 AC: 92479 AN: 150928 Hom.: 29189 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.613 AC: 92534 AN: 151046 Hom.: 29199 Cov.: 31 AF XY: 0.612 AC XY: 45174 AN XY: 73764

African (AFR) AF: 0.457 AC: 18875 AN: 41294

American (AMR) AF: 0.726 AC: 10980 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2193 AN: 3456

East Asian (EAS) AF: 0.779 AC: 3975 AN: 5102

South Asian (SAS) AF: 0.673 AC: 3241 AN: 4814

European-Finnish (FIN) AF: 0.609 AC: 6414 AN: 10524

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.662 AC: 44655 AN: 67428

Other (OTH) AF: 0.621 AC: 1303 AN: 2098

Alfa AF: 0.549 Hom.: 2416

Bravo AF: 0.616

Asia WGS AF: 0.690 AC: 2397 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.3
DANN	Benign	0.78
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs900554; hg19: chr2-145490097;