rs12697975

Positions:

• chr7-156515858-G-A
• chr7-156515858-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026865.2(RNF32-DT):​n.1782-34238C>T variant causes a intron, non coding transcript 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 NR_026865.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF32-DT	NR_026865.2	n.1782-34238C>T		intron_variant, non_coding_transcript_variant
RNF32-DT	NR_103858.1	n.146-43147C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF32-DT	ENST00000651649.1	n.258-43147C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.0834

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.220

Alfa AF: 0.199 Hom.: 627

Bravo AF: 0.224

Asia WGS AF: 0.203 AC: 706 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	1.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12697975; hg19: chr7-156308552;