chr2-145230530-T-G

Position:

• chr2-145230530-T-G

Variant summary

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

The XR_923410.3(LOC100505498):​n.10795-28656T>G 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 0.061 in 152,232 control chromosomes in the GnomAD database, including 723 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 0.061 (723 hom., cov: 32)
• Consequence: LOC100505498 XR_923410.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

Genes affected

LOC100505498 (HGNC:):

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100505498	XR_923410.3	n.10795-28656T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX41	ENST00000629218.2	n.621+5558T>G		intron_variant, non_coding_transcript_variant		5
TEX41	ENST00000630139.2	n.536-28656T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0610 AC: 9281 AN: 152114 Hom.: 720 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.00662

Gnomad EAS AF: 0.0428

Gnomad SAS AF: 0.0270

Gnomad FIN AF: 0.00188

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0610 AC: 9290 AN: 152232 Hom.: 723 Cov.: 32 AF XY: 0.0582 AC XY: 4336 AN XY: 74458

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.0437

Gnomad4 ASJ AF: 0.00662

Gnomad4 EAS AF: 0.0429

Gnomad4 SAS AF: 0.0262

Gnomad4 FIN AF: 0.00188

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0411 Hom.: 55

Bravo AF: 0.0688

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496975; hg19: chr2-145988098;