rs7500911

Variant names:

• chr16-29315608-A-C
• rs7500911
• ENST00000569730.1:n.240+3019A>C

Your query was ambiguous. Multiple possible variants found:

• chr16-29315608-A-C
• chr16-29315608-A-G

Variant summary

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

The ENST00000569730.1(ENSG00000260413):​n.240+3019A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,136 control chromosomes in the GnomAD database, including 6,640 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 0.29 (6640 hom., cov: 32)
• Consequence: ENSG00000260413 ENST00000569730.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 4 publications found

Genes affected

ENSG00000260413 (HGNC:):

RRN3P2 (HGNC:37619): (RRN3 pseudogene 2) Predicted to enable RNA polymerase I core binding activity and RNA polymerase I general transcription initiation factor activity. Predicted to be involved in transcription initiation from RNA polymerase I promoter. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SNX29P2 (HGNC:31914): (sorting nexin 29 pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX29P2	NR_002939.3	n.342+3019A>C		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260413	ENST00000569730.1	n.240+3019A>C		intron_variant	Intron 1 of 4	6
RRN3P2	ENST00000604430.1	n.999+3019A>C		intron_variant	Intron 3 of 10	5
RRN3P2	ENST00000641956.1	n.1006+3019A>C		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43347 AN: 152018 Hom.: 6628 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.285 AC: 43366 AN: 152136 Hom.: 6640 Cov.: 32 AF XY: 0.285 AC XY: 21180 AN XY: 74364

African (AFR) AF: 0.179 AC: 7437 AN: 41520

American (AMR) AF: 0.363 AC: 5545 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1067 AN: 3466

East Asian (EAS) AF: 0.350 AC: 1813 AN: 5182

South Asian (SAS) AF: 0.273 AC: 1317 AN: 4818

European-Finnish (FIN) AF: 0.356 AC: 3756 AN: 10556

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21383 AN: 67982

Other (OTH) AF: 0.297 AC: 628 AN: 2114

Alfa AF: 0.280 Hom.: 3585

Bravo AF: 0.286

Asia WGS AF: 0.261 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.78
DANN	Benign	0.42
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs7500911; hg19: chr16-29326929;