7-156515858-G-A

Variant names:

• chr7-156515858-G-A
• rs12697975
• ENST00000425712.1:n.146-43147C>T

Variant summary

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

The ENST00000425712.1(RNF32-DT):​n.146-43147C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 151,876 control chromosomes in the GnomAD database, including 4,667 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 0.23 (4667 hom., cov: 31)
• Consequence: RNF32-DT ENST00000425712.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768
• Publications: 2 publications found

Genes affected

RNF32-DT (HGNC:48971): (RNF32 divergent transcript) Predicted to be integral component of membrane. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425712.1. 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
	RNF32-DT	NR_026865.2		n.1782-34238C>T		intron	N/A
	RNF32-DT	NR_103858.1		n.146-43147C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF32-DT	ENST00000425712.1	TSL:2	n.146-43147C>T		intron	N/A
	RNF32-DT	ENST00000447933.7	TSL:3	n.343-43147C>T		intron	N/A
	RNF32-DT	ENST00000651649.1		n.258-43147C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35073 AN: 151758 Hom.: 4659 Cov.: 31

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0832

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.219

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.231 AC: 35107 AN: 151876 Hom.: 4667 Cov.: 31 AF XY: 0.231 AC XY: 17132 AN XY: 74206

African (AFR) AF: 0.133 AC: 5525 AN: 41478

American (AMR) AF: 0.279 AC: 4246 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 713 AN: 3470

East Asian (EAS) AF: 0.0834 AC: 432 AN: 5178

South Asian (SAS) AF: 0.303 AC: 1450 AN: 4788

European-Finnish (FIN) AF: 0.276 AC: 2904 AN: 10510

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19082 AN: 67914

Other (OTH) AF: 0.220 AC: 462 AN: 2098

Alfa AF: 0.197 Hom.: 639

Bravo AF: 0.224

Asia WGS AF: 0.203 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		-0.77

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12697975;

hg19: chr7-156308552;