rs10787728

Variant names:

• chr10-116750088-C-T
• rs10787728
• ENST00000437011.1:n.184C>T

Variant summary

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

The ENST00000437011.1(RPL5P27):​n.184C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.766 in 387,742 control chromosomes in the GnomAD database, including 118,636 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 0.71 (40921 hom., cov: 32)
  • Exomes 𝑓: 0.80 (77715 hom.)
• Consequence: RPL5P27 ENST00000437011.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.78
• Publications: 1 publications found

Genes affected

RPL5P27 (HGNC:36172): (ribosomal protein L5 pseudogene 27)

HSPA12A (HGNC:19022): (heat shock protein family A (Hsp70) member 12A) Predicted to enable ATP binding activity. Located in extracellular exosome. [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=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL5P27		n.116750088C>T		intragenic_variant
HSPA12A	NM_001330164.2	c.92-42803G>A		intron_variant	Intron 2 of 12		NP_001317093.1
HSPA12A	XM_005269673.6	c.89-42803G>A		intron_variant	Intron 2 of 12		XP_005269730.1
HSPA12A	XM_011539579.3	c.89-42803G>A		intron_variant	Intron 3 of 13		XP_011537881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL5P27	ENST00000437011.1	n.184C>T		non_coding_transcript_exon_variant	Exon 1 of 2	6
HSPA12A	ENST00000635765.1	c.92-42803G>A		intron_variant	Intron 2 of 12	5		ENSP00000489674.1
HSPA12A	ENST00000674197.1	c.89-42803G>A		intron_variant	Intron 2 of 12			ENSP00000501472.1

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107275 AN: 151980 Hom.: 40919 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.727

GnomAD4 exome AF: 0.804 AC: 189527 AN: 235644 Hom.: 77715 Cov.: 0 AF XY: 0.809 AC XY: 102056 AN XY: 126114

African (AFR) AF: 0.384 AC: 2885 AN: 7522

American (AMR) AF: 0.754 AC: 11228 AN: 14884

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 5706 AN: 6868

East Asian (EAS) AF: 0.597 AC: 10927 AN: 18288

South Asian (SAS) AF: 0.857 AC: 12822 AN: 14960

European-Finnish (FIN) AF: 0.881 AC: 14680 AN: 16658

Middle Eastern (MID) AF: 0.802 AC: 733 AN: 914

European-Non Finnish (NFE) AF: 0.843 AC: 119755 AN: 141998

Other (OTH) AF: 0.796 AC: 10791 AN: 13552

GnomAD4 genome AF: 0.705 AC: 107299 AN: 152098 Hom.: 40921 Cov.: 32 AF XY: 0.711 AC XY: 52836 AN XY: 74348

African (AFR) AF: 0.388 AC: 16079 AN: 41456

American (AMR) AF: 0.748 AC: 11444 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2841 AN: 3472

East Asian (EAS) AF: 0.609 AC: 3138 AN: 5154

South Asian (SAS) AF: 0.855 AC: 4111 AN: 4806

European-Finnish (FIN) AF: 0.892 AC: 9458 AN: 10602

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57589 AN: 68000

Other (OTH) AF: 0.727 AC: 1533 AN: 2108

Alfa AF: 0.784 Hom.: 93587

Bravo AF: 0.674

Asia WGS AF: 0.692 AC: 2406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		4.8

Splicing

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

Other links and lift over

dbSNP: rs10787728; hg19: chr10-118509599; COSMIC: COSV70898055;