rs2065914

Variant names:

• chr1-240007496-T-C
• rs2065914
• ENST00000668221.1:n.-28T>C

Variant summary

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

The ENST00000668221.1(RPS7P5):​n.-28T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,778 control chromosomes in the GnomAD database, including 11,754 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 (11754 hom., cov: 31)
• Consequence: RPS7P5 ENST00000668221.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 1 publications found

Genes affected

RPS7P5 (HGNC:):

RPS7P5 (HGNC:37037): (ribosomal protein S7 pseudogene 5)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPS7P5	NR_036695.2	n.-28T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPS7P5	ENST00000668221.1	n.-28T>C		upstream_gene_variant
RPS7P5	ENST00000833953.1	n.-6T>C		upstream_gene_variant
RPS7P5	ENST00000833954.1	n.-28T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58736 AN: 151660 Hom.: 11755 Cov.: 31

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.387 AC: 58746 AN: 151778 Hom.: 11754 Cov.: 31 AF XY: 0.385 AC XY: 28577 AN XY: 74152

African (AFR) AF: 0.338 AC: 13970 AN: 41376

American (AMR) AF: 0.318 AC: 4839 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1673 AN: 3464

East Asian (EAS) AF: 0.206 AC: 1059 AN: 5136

South Asian (SAS) AF: 0.373 AC: 1784 AN: 4788

European-Finnish (FIN) AF: 0.410 AC: 4306 AN: 10514

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29827 AN: 67960

Other (OTH) AF: 0.390 AC: 821 AN: 2104

Alfa AF: 0.416 Hom.: 23141

Bravo AF: 0.375

Asia WGS AF: 0.277 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2065914; hg19: chr1-240170796;