rs786255

chr2-144934149-G-Achr2-144934149-G-Cchr2-144934149-G-T

Variant summary

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

The NR_033870.2(TEX41):n.463+30346G>A 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 0.596 in 151,862 control chromosomes in the GnomAD database, including 27,821 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 0.60 (27821 hom., cov: 32)
• Consequence: TEX41 NR_033870.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX41	NR_033870.2	n.463+30346G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX41	ENST00000653533.1	n.728+30346G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90523 AN: 151742 Hom.: 27809 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.596 AC: 90565 AN: 151862 Hom.: 27821 Cov.: 32 AF XY: 0.602 AC XY: 44678 AN XY: 74200

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.573

Alfa AF: 0.604 Hom.: 3381

Bravo AF: 0.595

Asia WGS AF: 0.803 AC: 2788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.95
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs786255; hg19: chr2-145691716;