rs2675705

Variant names:

• chr10-86631504-C-T
• rs2675705
• ENST00000481963.1:n.125G>A

Variant summary

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

The ENST00000481963.1(RPL7AP8):​n.125G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.291 in 921,162 control chromosomes in the GnomAD database, including 41,292 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 0.30 (6874 hom., cov: 32)
  • Exomes 𝑓: 0.29 (34418 hom.)
• Consequence: RPL7AP8 ENST00000481963.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.72
• Publications: 1 publications found

Genes affected

RPL7AP8 (HGNC:23738): (ribosomal protein L7a pseudogene 8)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000481963.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL7AP8	ENST00000481963.1	TSL:6	n.125G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45065 AN: 151888 Hom.: 6864 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.301

GnomAD4 exome AF: 0.290 AC: 222791 AN: 769156 Hom.: 34418 Cov.: 10 AF XY: 0.286 AC XY: 116891 AN XY: 408058

African (AFR) AF: 0.278 AC: 5620 AN: 20202

American (AMR) AF: 0.373 AC: 15459 AN: 41396

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 6176 AN: 21526

East Asian (EAS) AF: 0.523 AC: 18887 AN: 36104

South Asian (SAS) AF: 0.253 AC: 17959 AN: 71054

European-Finnish (FIN) AF: 0.290 AC: 10625 AN: 36620

Middle Eastern (MID) AF: 0.287 AC: 906 AN: 3158

European-Non Finnish (NFE) AF: 0.271 AC: 135924 AN: 501482

Other (OTH) AF: 0.299 AC: 11235 AN: 37614

GnomAD4 genome AF: 0.297 AC: 45094 AN: 152006 Hom.: 6874 Cov.: 32 AF XY: 0.300 AC XY: 22297 AN XY: 74280

African (AFR) AF: 0.290 AC: 12040 AN: 41474

American (AMR) AF: 0.361 AC: 5521 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3472

East Asian (EAS) AF: 0.510 AC: 2618 AN: 5136

South Asian (SAS) AF: 0.278 AC: 1335 AN: 4800

European-Finnish (FIN) AF: 0.275 AC: 2909 AN: 10576

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.274 AC: 18589 AN: 67960

Other (OTH) AF: 0.298 AC: 629 AN: 2108

Alfa AF: 0.281 Hom.: 761

Bravo AF: 0.306

Asia WGS AF: 0.376 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	2.9
DANN	Benign	0.69
PhyloP100		3.7

Splicing

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

Other links and lift over

dbSNP: rs2675705; hg19: chr10-88391261;