10-37856581-A-G

Variant summary

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

The ENST00000611278.4(ZNF248):​c.-271T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,142,014 control chromosomes in the GnomAD database, including 11,443 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 ( 1353 hom., cov: 32)
Exomes 𝑓: 0.14 ( 10090 hom. )

Consequence

ZNF248
ENST00000611278.4 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.332
Variant links:
Genes affected
ZNF248 (HGNC:13041): (zinc finger protein 248) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [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=-0.88).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ZNF248NM_021045.3 linkuse as main transcriptc.-125-49T>C intron_variant ENST00000395867.8 NP_066383.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZNF248ENST00000395867.8 linkuse as main transcriptc.-125-49T>C intron_variant 1 NM_021045.3 ENSP00000379208 P1Q8NDW4-1

Frequencies

GnomAD3 genomes
AF:
0.129
AC:
19539
AN:
151950
Hom.:
1352
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.104
Gnomad AMI
AF:
0.126
Gnomad AMR
AF:
0.195
Gnomad ASJ
AF:
0.141
Gnomad EAS
AF:
0.104
Gnomad SAS
AF:
0.0628
Gnomad FIN
AF:
0.0916
Gnomad MID
AF:
0.149
Gnomad NFE
AF:
0.140
Gnomad OTH
AF:
0.144
GnomAD4 exome
AF:
0.141
AC:
139190
AN:
989946
Hom.:
10090
Cov.:
29
AF XY:
0.141
AC XY:
65422
AN XY:
465050
show subpopulations
Gnomad4 AFR exome
AF:
0.0927
Gnomad4 AMR exome
AF:
0.189
Gnomad4 ASJ exome
AF:
0.134
Gnomad4 EAS exome
AF:
0.103
Gnomad4 SAS exome
AF:
0.0656
Gnomad4 FIN exome
AF:
0.0760
Gnomad4 NFE exome
AF:
0.145
Gnomad4 OTH exome
AF:
0.131
GnomAD4 genome
AF:
0.129
AC:
19544
AN:
152068
Hom.:
1353
Cov.:
32
AF XY:
0.128
AC XY:
9521
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.104
Gnomad4 AMR
AF:
0.195
Gnomad4 ASJ
AF:
0.141
Gnomad4 EAS
AF:
0.103
Gnomad4 SAS
AF:
0.0624
Gnomad4 FIN
AF:
0.0916
Gnomad4 NFE
AF:
0.140
Gnomad4 OTH
AF:
0.143
Alfa
AF:
0.132
Hom.:
158
Bravo
AF:
0.139
Asia WGS
AF:
0.0860
AC:
298
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
12
DANN
Benign
0.73

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs1322319; hg19: chr10-38145509; API