rs7680948

Variant summary

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

The NM_030648.4(SETD7):​c.563-2516T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,130 control chromosomes in the GnomAD database, including 6,973 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 0.30 ( 6973 hom., cov: 32)

Consequence

SETD7
NM_030648.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.579
Variant links:
Genes affected
SETD7 (HGNC:30412): (SET domain containing 7, histone lysine methyltransferase) Enables histone-lysine N-methyltransferase activity and p53 binding activity. Involved in peptidyl-lysine dimethylation and peptidyl-lysine monomethylation. Acts upstream of or within cellular response to DNA damage stimulus and heterochromatin organization. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

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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 (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SETD7NM_030648.4 linkuse as main transcriptc.563-2516T>G intron_variant ENST00000274031.8 NP_085151.1
SETD7NM_001306199.2 linkuse as main transcriptc.563-2516T>G intron_variant NP_001293128.1
SETD7XM_017008661.1 linkuse as main transcriptc.149-2516T>G intron_variant XP_016864150.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SETD7ENST00000274031.8 linkuse as main transcriptc.563-2516T>G intron_variant 1 NM_030648.4 ENSP00000274031 P1
SETD7ENST00000506866.6 linkuse as main transcriptc.563-2516T>G intron_variant 1 ENSP00000427300

Frequencies

GnomAD3 genomes
AF:
0.297
AC:
45119
AN:
152012
Hom.:
6964
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.355
Gnomad AMI
AF:
0.221
Gnomad AMR
AF:
0.285
Gnomad ASJ
AF:
0.220
Gnomad EAS
AF:
0.468
Gnomad SAS
AF:
0.284
Gnomad FIN
AF:
0.238
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.266
Gnomad OTH
AF:
0.303
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.297
AC:
45164
AN:
152130
Hom.:
6973
Cov.:
32
AF XY:
0.296
AC XY:
22002
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.354
Gnomad4 AMR
AF:
0.285
Gnomad4 ASJ
AF:
0.220
Gnomad4 EAS
AF:
0.469
Gnomad4 SAS
AF:
0.285
Gnomad4 FIN
AF:
0.238
Gnomad4 NFE
AF:
0.266
Gnomad4 OTH
AF:
0.303
Alfa
AF:
0.275
Hom.:
5793
Bravo
AF:
0.304
Asia WGS
AF:
0.387
AC:
1345
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
1.6
DANN
Benign
0.49

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: rs7680948; hg19: chr4-140447105; API