2-144995599-G-T

Variant names:

• chr2-144995599-G-T
• rs1371048
• ENST00000445791.5:n.308-75221G>T

Variant summary

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

The ENST00000445791.5(TEX41):​n.308-75221G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,006 control chromosomes in the GnomAD database, including 12,092 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 0.37 (12092 hom., cov: 32)
• Consequence: TEX41 ENST00000445791.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454
• Publications: 10 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 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.464-75221G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX41	ENST00000445791.5	TSL:1	n.308-75221G>T		intron	N/A
	TEX41	ENST00000451774.5	TSL:1	n.405-75221G>T		intron	N/A
	TEX41	ENST00000451027.5	TSL:4	n.469-48767G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56271 AN: 151888 Hom.: 12077 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.370 AC: 56305 AN: 152006 Hom.: 12092 Cov.: 32 AF XY: 0.378 AC XY: 28100 AN XY: 74296

African (AFR) AF: 0.236 AC: 9799 AN: 41444

American (AMR) AF: 0.509 AC: 7772 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1310 AN: 3468

East Asian (EAS) AF: 0.975 AC: 5046 AN: 5178

South Asian (SAS) AF: 0.506 AC: 2437 AN: 4814

European-Finnish (FIN) AF: 0.366 AC: 3860 AN: 10538

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24776 AN: 67970

Other (OTH) AF: 0.356 AC: 751 AN: 2112

Alfa AF: 0.305 Hom.: 1357

Bravo AF: 0.380

Asia WGS AF: 0.707 AC: 2452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.24
DANN	Benign	0.45
PhyloP100		-0.45

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1371048;

hg19: chr2-145753166;