rs2071495

Variant summary

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

The XR_007065537.1(LOC124903876):​n.282+5747C>G 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 0.13 in 152,704 control chromosomes in the GnomAD database, including 2,112 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 0.13 ( 2107 hom., cov: 32)
Exomes 𝑓: 0.12 ( 5 hom. )

Consequence

LOC124903876
XR_007065537.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.155
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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124903876XR_007065537.1 linkuse as main transcriptn.282+5747C>G intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.130
AC:
19839
AN:
152136
Hom.:
2112
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0309
Gnomad AMI
AF:
0.387
Gnomad AMR
AF:
0.145
Gnomad ASJ
AF:
0.255
Gnomad EAS
AF:
0.569
Gnomad SAS
AF:
0.108
Gnomad FIN
AF:
0.101
Gnomad MID
AF:
0.196
Gnomad NFE
AF:
0.149
Gnomad OTH
AF:
0.175
GnomAD4 exome
AF:
0.124
AC:
56
AN:
450
Hom.:
5
AF XY:
0.112
AC XY:
31
AN XY:
276
show subpopulations
Gnomad4 FIN exome
AF:
0.114
Gnomad4 NFE exome
AF:
0.313
Gnomad4 OTH exome
AF:
0.250
GnomAD4 genome
AF:
0.130
AC:
19825
AN:
152254
Hom.:
2107
Cov.:
32
AF XY:
0.131
AC XY:
9715
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.0308
Gnomad4 AMR
AF:
0.145
Gnomad4 ASJ
AF:
0.255
Gnomad4 EAS
AF:
0.568
Gnomad4 SAS
AF:
0.107
Gnomad4 FIN
AF:
0.101
Gnomad4 NFE
AF:
0.149
Gnomad4 OTH
AF:
0.178
Alfa
AF:
0.137
Hom.:
240
Bravo
AF:
0.136
Asia WGS
AF:
0.287
AC:
997
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
7.5
DANN
Benign
0.34

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: rs2071495; hg19: chr1-23884333; API