chr10-86631504-C-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL7AP8		n.86631504C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL7AP8	ENST00000481963.1	n.125G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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;