rs1822620

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_923410.3(LOC100505498):​n.10795-30236G>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 0.0417 in 152,188 control chromosomes in the GnomAD database, including 296 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 0.042 ( 296 hom., cov: 32)

Consequence

LOC100505498
XR_923410.3 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0890
Variant links:
Genes affected
TEX41 (HGNC:48667): (testis expressed 41)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC100505498XR_923410.3 linkuse as main transcriptn.10795-30236G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TEX41ENST00000629218.2 linkuse as main transcriptn.621+3978G>A intron_variant, non_coding_transcript_variant 5
TEX41ENST00000630139.2 linkuse as main transcriptn.536-30236G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0417
AC:
6344
AN:
152070
Hom.:
294
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.112
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0355
Gnomad ASJ
AF:
0.00664
Gnomad EAS
AF:
0.0431
Gnomad SAS
AF:
0.0267
Gnomad FIN
AF:
0.00189
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.0101
Gnomad OTH
AF:
0.0283
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0417
AC:
6349
AN:
152188
Hom.:
296
Cov.:
32
AF XY:
0.0400
AC XY:
2974
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.112
Gnomad4 AMR
AF:
0.0354
Gnomad4 ASJ
AF:
0.00664
Gnomad4 EAS
AF:
0.0432
Gnomad4 SAS
AF:
0.0259
Gnomad4 FIN
AF:
0.00189
Gnomad4 NFE
AF:
0.0101
Gnomad4 OTH
AF:
0.0289
Alfa
AF:
0.0156
Hom.:
93
Bravo
AF:
0.0469
Asia WGS
AF:
0.0520
AC:
183
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.5
DANN
Benign
0.55

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1822620; hg19: chr2-145986518; API