rs1609163

chr7-156629361-A-G

Variant summary

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

The NR_026865.2(RNF32-DT):n.1588+9587T>C 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 0.0785 in 152,244 control chromosomes in the GnomAD database, including 890 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 0.079 (890 hom., cov: 33)
• Consequence: RNF32-DT NR_026865.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF32-DT	NR_026865.2	n.1588+9587T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF32-DT	ENST00000651649.1	n.64+11175T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0784 AC: 11929 AN: 152126 Hom.: 886 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0613

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.0454

Gnomad FIN AF: 0.0527

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0187

Gnomad OTH AF: 0.0665

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

GnomAD4 genome AF: 0.0785 AC: 11955 AN: 152244 Hom.: 890 Cov.: 33 AF XY: 0.0792 AC XY: 5897 AN XY: 74444

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.0616

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.0452

Gnomad4 FIN AF: 0.0527

Gnomad4 NFE AF: 0.0187

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0529 Hom.: 64

Bravo AF: 0.0883

Asia WGS AF: 0.123 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.8
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1609163; hg19: chr7-156422055;