rs2315504

Variant summary

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

The XR_934754.3(LOC105371777):​n.64-27600C>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 0.673 in 152,012 control chromosomes in the GnomAD database, including 35,822 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 0.67 ( 35822 hom., cov: 32)

Consequence

LOC105371777
XR_934754.3 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07
Variant links:
Genes affected

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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105371777XR_934754.3 linkuse as main transcriptn.64-27600C>A intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.672
AC:
102136
AN:
151896
Hom.:
35774
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.845
Gnomad AMI
AF:
0.577
Gnomad AMR
AF:
0.687
Gnomad ASJ
AF:
0.587
Gnomad EAS
AF:
0.983
Gnomad SAS
AF:
0.669
Gnomad FIN
AF:
0.645
Gnomad MID
AF:
0.579
Gnomad NFE
AF:
0.552
Gnomad OTH
AF:
0.625
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.673
AC:
102234
AN:
152012
Hom.:
35822
Cov.:
32
AF XY:
0.680
AC XY:
50520
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.846
Gnomad4 AMR
AF:
0.688
Gnomad4 ASJ
AF:
0.587
Gnomad4 EAS
AF:
0.983
Gnomad4 SAS
AF:
0.668
Gnomad4 FIN
AF:
0.645
Gnomad4 NFE
AF:
0.552
Gnomad4 OTH
AF:
0.624
Alfa
AF:
0.573
Hom.:
47844
Bravo
AF:
0.681
Asia WGS
AF:
0.794
AC:
2761
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
0.057
DANN
Benign
0.40

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: rs2315504; hg19: chr17-39046881; API