rs768763

Variant summary

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

The XR_007058748.1(LOC102723740):​n.116+1381T>C 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 0.146 in 152,174 control chromosomes in the GnomAD database, including 1,887 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 0.15 ( 1887 hom., cov: 31)

Consequence

LOC102723740
XR_007058748.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.11
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC102723740XR_007058748.1 linkuse as main transcriptn.116+1381T>C intron_variant, non_coding_transcript_variant
LOC124900969XR_007058749.1 linkuse as main transcriptn.64-4432A>G intron_variant, non_coding_transcript_variant
LOC102723740XR_925953.3 linkuse as main transcriptn.247+549T>C intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.146
AC:
22205
AN:
152054
Hom.:
1892
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0490
Gnomad AMI
AF:
0.193
Gnomad AMR
AF:
0.145
Gnomad ASJ
AF:
0.164
Gnomad EAS
AF:
0.231
Gnomad SAS
AF:
0.200
Gnomad FIN
AF:
0.183
Gnomad MID
AF:
0.256
Gnomad NFE
AF:
0.187
Gnomad OTH
AF:
0.166
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.146
AC:
22195
AN:
152174
Hom.:
1887
Cov.:
31
AF XY:
0.147
AC XY:
10935
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.0490
Gnomad4 AMR
AF:
0.144
Gnomad4 ASJ
AF:
0.164
Gnomad4 EAS
AF:
0.231
Gnomad4 SAS
AF:
0.200
Gnomad4 FIN
AF:
0.183
Gnomad4 NFE
AF:
0.187
Gnomad4 OTH
AF:
0.164
Alfa
AF:
0.178
Hom.:
3636
Bravo
AF:
0.139
Asia WGS
AF:
0.203
AC:
709
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
7.3
DANN
Benign
0.62

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: rs768763; hg19: chr5-41293370; API