chr7-1022730-T-C

Variant summary

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

The NM_001318252.2(C7orf50):​c.130-12587A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,066 control chromosomes in the GnomAD database, including 3,116 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 0.20 ( 3116 hom., cov: 33)

Consequence

C7orf50
NM_001318252.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.852
Variant links:
Genes affected
C7orf50 (HGNC:22421): (chromosome 7 open reading frame 50) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
C7orf50NM_001318252.2 linkuse as main transcriptc.130-12587A>G intron_variant ENST00000397098.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
C7orf50ENST00000397098.8 linkuse as main transcriptc.130-12587A>G intron_variant 1 NM_001318252.2 P1

Frequencies

GnomAD3 genomes
AF:
0.196
AC:
29819
AN:
151948
Hom.:
3112
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.161
Gnomad AMI
AF:
0.176
Gnomad AMR
AF:
0.237
Gnomad ASJ
AF:
0.141
Gnomad EAS
AF:
0.132
Gnomad SAS
AF:
0.148
Gnomad FIN
AF:
0.265
Gnomad MID
AF:
0.136
Gnomad NFE
AF:
0.210
Gnomad OTH
AF:
0.197
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.196
AC:
29838
AN:
152066
Hom.:
3116
Cov.:
33
AF XY:
0.197
AC XY:
14617
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.161
Gnomad4 AMR
AF:
0.237
Gnomad4 ASJ
AF:
0.141
Gnomad4 EAS
AF:
0.132
Gnomad4 SAS
AF:
0.148
Gnomad4 FIN
AF:
0.265
Gnomad4 NFE
AF:
0.210
Gnomad4 OTH
AF:
0.194
Alfa
AF:
0.186
Hom.:
1403
Bravo
AF:
0.193
Asia WGS
AF:
0.136
AC:
472
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.91
DANN
Benign
0.62

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: rs1057558; hg19: chr7-1062366; API