rs7971637

Variant summary

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

The XR_002957397.2(GAPDH-DT):​n.245G>A 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 0.172 in 154,472 control chromosomes in the GnomAD database, including 2,504 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 0.17 ( 2469 hom., cov: 33)
Exomes 𝑓: 0.13 ( 35 hom. )

Consequence

GAPDH-DT
XR_002957397.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.923
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=-0.81).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GAPDH-DTXR_002957397.2 linkuse as main transcriptn.245G>A non_coding_transcript_exon_variant 1/2
use as main transcriptn.6534163C>T intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.173
AC:
26325
AN:
152050
Hom.:
2472
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.114
Gnomad AMI
AF:
0.246
Gnomad AMR
AF:
0.201
Gnomad ASJ
AF:
0.0848
Gnomad EAS
AF:
0.307
Gnomad SAS
AF:
0.123
Gnomad FIN
AF:
0.207
Gnomad MID
AF:
0.104
Gnomad NFE
AF:
0.195
Gnomad OTH
AF:
0.164
GnomAD4 exome
AF:
0.135
AC:
310
AN:
2304
Hom.:
35
Cov.:
0
AF XY:
0.126
AC XY:
185
AN XY:
1472
show subpopulations
Gnomad4 AFR exome
AF:
0.167
Gnomad4 AMR exome
AF:
0.134
Gnomad4 ASJ exome
AF:
0.100
Gnomad4 EAS exome
AF:
0.136
Gnomad4 SAS exome
AF:
0.0781
Gnomad4 FIN exome
AF:
0.192
Gnomad4 NFE exome
AF:
0.156
Gnomad4 OTH exome
AF:
0.128
GnomAD4 genome
AF:
0.173
AC:
26327
AN:
152168
Hom.:
2469
Cov.:
33
AF XY:
0.173
AC XY:
12865
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.114
Gnomad4 AMR
AF:
0.200
Gnomad4 ASJ
AF:
0.0848
Gnomad4 EAS
AF:
0.307
Gnomad4 SAS
AF:
0.123
Gnomad4 FIN
AF:
0.207
Gnomad4 NFE
AF:
0.195
Gnomad4 OTH
AF:
0.162
Alfa
AF:
0.186
Hom.:
1192
Bravo
AF:
0.173
Asia WGS
AF:
0.219
AC:
761
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
12
DANN
Benign
0.84

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs7971637; hg19: chr12-6643329; API