rs7795368

Variant names:

• chr7-156636942-C-A
• rs7795368
• ENST00000418309.2:n.61+3594G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-156636942-C-A
• chr7-156636942-C-T

Variant summary

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

The ENST00000440711.2(RNF32-DT):​n.81+3594G>T variant causes a intron 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 ENST00000440711.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440711.2. 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
	RNF32-DT	NR_026865.2		n.1588+2006G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF32-DT	ENST00000418309.2	TSL:3	n.61+3594G>T		intron	N/A
	RNF32-DT	ENST00000440711.2	TSL:2	n.81+3594G>T		intron	N/A
	RNF32-DT	ENST00000447933.7	TSL:3	n.42+3594G>T		intron	N/A

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

African (AFR) AF: 0.550 AC: 22754 AN: 41334

American (AMR) AF: 0.417 AC: 6358 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3468

East Asian (EAS) AF: 0.371 AC: 1914 AN: 5160

South Asian (SAS) AF: 0.262 AC: 1262 AN: 4812

European-Finnish (FIN) AF: 0.383 AC: 4032 AN: 10518

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21332 AN: 67898

Other (OTH) AF: 0.354 AC: 741 AN: 2094

Alfa AF: 0.376 Hom.: 1837

Bravo AF: 0.401

Asia WGS AF: 0.327 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs7795368; hg19: chr7-156429636;