rs1609163

Variant names:

• chr7-156629361-A-G
• rs1609163
• ENST00000418309.2:n.61+11175T>C

Variant summary

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

The ENST00000418309.2(RNF32-DT):​n.61+11175T>C variant causes a intron 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 ENST00000418309.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 3 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=-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 rank	MANE	Protein	UniProt
RNF32-DT	NR_026865.2	n.1588+9587T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF32-DT	ENST00000418309.2	n.61+11175T>C		intron_variant	Intron 1 of 3	3
RNF32-DT	ENST00000440711.2	n.81+11175T>C		intron_variant	Intron 1 of 2	2
RNF32-DT	ENST00000447933.7	n.42+11175T>C		intron_variant	Intron 1 of 3	3

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

African (AFR) AF: 0.181 AC: 7495 AN: 41516

American (AMR) AF: 0.0616 AC: 943 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3472

East Asian (EAS) AF: 0.220 AC: 1137 AN: 5176

South Asian (SAS) AF: 0.0452 AC: 218 AN: 4824

European-Finnish (FIN) AF: 0.0527 AC: 559 AN: 10604

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0187 AC: 1270 AN: 68030

Other (OTH) AF: 0.0668 AC: 141 AN: 2112

Alfa AF: 0.0341 Hom.: 293

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1609163; hg19: chr7-156422055;