rs2252641

chr2-145043894-T-Cchr2-145043894-T-G

Variant summary

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

The NR_033870.2(TEX41):n.464-26926T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,994 control chromosomes in the GnomAD database, including 27,397 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 0.58 (27396 hom., cov: 32)
  • Exomes 𝑓: 0.36 (1 hom.)
• Consequence: TEX41 NR_033870.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.54

Genes affected

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

LOC100505498 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX41	NR_033870.2	n.464-26926T>C		intron_variant, non_coding_transcript_variant
LOC100505498	XR_923410.3	n.5785+20621T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX41	ENST00000653533.1	n.729-128104T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87710 AN: 151864 Hom.: 27348 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.562

GnomAD4 exome AF: 0.357 AC: 5 AN: 14 Hom.: 1 Cov.: 0 AF XY: 0.357 AC XY: 5 AN XY: 14

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.400

GnomAD4 genome AF: 0.578 AC: 87817 AN: 151980 Hom.: 27396 Cov.: 32 AF XY: 0.579 AC XY: 42957 AN XY: 74254

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.567

Alfa AF: 0.478 Hom.: 39524

Bravo AF: 0.598

Asia WGS AF: 0.704 AC: 2448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.071
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2252641; hg19: chr2-145801461;