4-139496317-G-T

Variant names:

• chr4-139496317-G-T
• rs4863655
• ENST00000506866.7:c.*36C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001306199.2(SETD7):​c.*36C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 692,882 control chromosomes in the GnomAD database, including 254,255 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 0.83 (52290 hom., cov: 31)
  • Exomes 𝑓: 0.86 (201965 hom.)
• Consequence: SETD7 NM_001306199.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 14 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001306199.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SETD7	NM_001306199.2		c.*36C>A		3_prime_UTR	Exon 8 of 8	NP_001293128.1	D6RJA0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SETD7	ENST00000506866.7	TSL:1	c.*36C>A		3_prime_UTR	Exon 8 of 8	ENSP00000427300.1	D6RJA0
	SETD7	ENST00000515101.1	TSL:3	n.483C>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125546 AN: 151988 Hom.: 52244 Cov.: 31

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.829

GnomAD2 exomes AF: 0.848 AC: 103216 AN: 121694 AF XY: 0.854

Gnomad AFR exome AF: 0.727

Gnomad AMR exome AF: 0.757

Gnomad ASJ exome AF: 0.833

Gnomad EAS exome AF: 0.986

Gnomad FIN exome AF: 0.897

Gnomad NFE exome AF: 0.858

Gnomad OTH exome AF: 0.867

GnomAD4 exome AF: 0.863 AC: 466458 AN: 540776 Hom.: 201965 Cov.: 0 AF XY: 0.865 AC XY: 253023 AN XY: 292462

African (AFR) AF: 0.727 AC: 11133 AN: 15306

American (AMR) AF: 0.763 AC: 25404 AN: 33300

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 16323 AN: 19594

East Asian (EAS) AF: 0.978 AC: 31184 AN: 31888

South Asian (SAS) AF: 0.887 AC: 54132 AN: 60994

European-Finnish (FIN) AF: 0.898 AC: 29619 AN: 32992

Middle Eastern (MID) AF: 0.921 AC: 3703 AN: 4022

European-Non Finnish (NFE) AF: 0.861 AC: 269065 AN: 312498

Other (OTH) AF: 0.858 AC: 25895 AN: 30182

GnomAD4 genome AF: 0.826 AC: 125649 AN: 152106 Hom.: 52290 Cov.: 31 AF XY: 0.834 AC XY: 62002 AN XY: 74366

African (AFR) AF: 0.723 AC: 29976 AN: 41452

American (AMR) AF: 0.814 AC: 12446 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2906 AN: 3470

East Asian (EAS) AF: 0.982 AC: 5077 AN: 5172

South Asian (SAS) AF: 0.895 AC: 4311 AN: 4816

European-Finnish (FIN) AF: 0.909 AC: 9631 AN: 10598

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58447 AN: 67996

Other (OTH) AF: 0.831 AC: 1754 AN: 2110

Alfa AF: 0.848 Hom.: 90697

Bravo AF: 0.812

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.88
DANN	Benign	0.45
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4863655; hg19: chr4-140417471;