rs7795368

Positions:

• chr7-156636942-C-A

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+2006G>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 0.392 in 151,724 control chromosomes in the GnomAD database, including 12,540 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 0.39 (12540 hom., cov: 32)
• Consequence: RNF32-DT NR_026865.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF32-DT	NR_026865.2	n.1588+2006G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNF32-DT	ENST00000651649.1	n.64+3594G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59457 AN: 151606 Hom.: 12521 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.392 AC: 59509 AN: 151724 Hom.: 12540 Cov.: 32 AF XY: 0.394 AC XY: 29206 AN XY: 74124

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.354

Alfa AF: 0.371 Hom.: 1723

Bravo AF: 0.401

Asia WGS AF: 0.327 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7795368; hg19: chr7-156429636;