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GeneBe

rs10795668

Variant summary

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

The XR_001747277.2(LOC105376400):n.99-40C>T 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 0.246 in 152,092 control chromosomes in the GnomAD database, including 5,644 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 0.25 ( 5644 hom., cov: 32)

Consequence

LOC105376400
XR_001747277.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240
Variant links:
Genes affected

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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 (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105376400XR_001747277.2 linkuse as main transcriptn.99-40C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.246
AC:
37314
AN:
151976
Hom.:
5627
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0607
Gnomad AMI
AF:
0.352
Gnomad AMR
AF:
0.311
Gnomad ASJ
AF:
0.305
Gnomad EAS
AF:
0.368
Gnomad SAS
AF:
0.247
Gnomad FIN
AF:
0.292
Gnomad MID
AF:
0.291
Gnomad NFE
AF:
0.321
Gnomad OTH
AF:
0.273
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.246
AC:
37340
AN:
152092
Hom.:
5644
Cov.:
32
AF XY:
0.247
AC XY:
18331
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.0605
Gnomad4 AMR
AF:
0.311
Gnomad4 ASJ
AF:
0.305
Gnomad4 EAS
AF:
0.369
Gnomad4 SAS
AF:
0.248
Gnomad4 FIN
AF:
0.292
Gnomad4 NFE
AF:
0.321
Gnomad4 OTH
AF:
0.277
Alfa
AF:
0.309
Hom.:
16705
Bravo
AF:
0.239
Asia WGS
AF:
0.299
AC:
1040
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
1.7
Dann
Benign
0.33

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: rs10795668; hg19: chr10-8701219; API