rs923828
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_120450.1(LOC101927583):n.193C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 1,600,702 control chromosomes in the GnomAD database, including 128,355 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 0.34 ( 9660 hom., cov: 33)
Exomes 𝑓: 0.40 ( 118695 hom. )
Consequence
LOC101927583
NR_120450.1 non_coding_transcript_exon
NR_120450.1 non_coding_transcript_exon
Scores
3
15
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.84
Genes affected
SLC26A10P (HGNC:14470): (solute carrier family 26 member 10, pseudogene) Predicted to enable anion transmembrane transporter activity. Predicted to be involved in anion transport. Predicted to be active in basolateral plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0037638843).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC101927583 | NR_120450.1 | n.193C>T | non_coding_transcript_exon_variant | 1/4 | |||
SLC26A10P | NR_166679.1 | n.1271G>A | non_coding_transcript_exon_variant | 4/16 | |||
SLC26A10P | NR_166678.1 | n.1271G>A | non_coding_transcript_exon_variant | 4/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000440686.5 | n.449G>A | non_coding_transcript_exon_variant | 4/16 | 2 | |||||
SLC26A10P | ENST00000665594.1 | n.808G>A | non_coding_transcript_exon_variant | 5/18 |
Frequencies
GnomAD3 genomes ? AF: 0.335 AC: 50999AN: 152034Hom.: 9666 Cov.: 33
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.346 AC: 77879AN: 224952Hom.: 14642 AF XY: 0.352 AC XY: 43205AN XY: 122826
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GnomAD4 exome AF: 0.397 AC: 574607AN: 1448550Hom.: 118695 Cov.: 50 AF XY: 0.395 AC XY: 283864AN XY: 719088
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GnomAD4 genome ? AF: 0.335 AC: 50994AN: 152152Hom.: 9660 Cov.: 33 AF XY: 0.330 AC XY: 24548AN XY: 74386
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1647
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1662
ESP6500AA
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818
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3729
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39989
Asia WGS
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846
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
P;P
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at