rs955944

chr2-145055594-A-C

Variant summary

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

The NR_033870.2(TEX41):n.464-15226A>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 0.0183 in 152,258 control chromosomes in the GnomAD database, including 210 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 0.018 (210 hom., cov: 32)
• Consequence: TEX41 NR_033870.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX41	NR_033870.2	n.464-15226A>C		intron_variant, non_coding_transcript_variant
LOC100505498	XR_923410.3	n.5785+32321A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX41	ENST00000653533.1	n.729-116404A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0183 AC: 2788 AN: 152140 Hom.: 211 Cov.: 32

Gnomad AFR AF: 0.00309

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.00415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000235

Gnomad OTH AF: 0.0229

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

GnomAD4 genome AF: 0.0183 AC: 2787 AN: 152258 Hom.: 210 Cov.: 32 AF XY: 0.0204 AC XY: 1517 AN XY: 74442

Gnomad4 AFR AF: 0.00308

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0892

Gnomad4 SAS AF: 0.00373

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000235

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0345 Hom.: 76

Bravo AF: 0.0309

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.2
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs955944; hg19: chr2-145813161;