10-6071819-C-T

Variant names:

• chr10-6071819-C-T
• rs1887027
• ENST00000397237.2:n.100G>A

Variant summary

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

The ENST00000397237.2(RPL32P23):​n.100G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,292 control chromosomes in the GnomAD database, including 4,753 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 0.24 (4745 hom., cov: 32)
  • Exomes 𝑓: 0.21 (8 hom.)
• Consequence: RPL32P23 ENST00000397237.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.22
• Publications: 18 publications found

Genes affected

RPL32P23 (HGNC:36007): (ribosomal protein L32 pseudogene 23)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000397237.2. 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
	RPL32P23	ENST00000397237.2	TSL:6	n.100G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37089 AN: 151936 Hom.: 4730 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.249

GnomAD4 exome AF: 0.206 AC: 49 AN: 238 Hom.: 8 Cov.: 0 AF XY: 0.222 AC XY: 35 AN XY: 158

African (AFR) AF: 0.500 AC: 2 AN: 4

American (AMR) AF: 0.500 AC: 2 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.100 AC: 1 AN: 10

European-Finnish (FIN) AF: 0.195 AC: 16 AN: 82

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.197 AC: 24 AN: 122

Other (OTH) AF: 0.250 AC: 3 AN: 12

GnomAD4 genome AF: 0.244 AC: 37137 AN: 152054 Hom.: 4745 Cov.: 32 AF XY: 0.245 AC XY: 18224 AN XY: 74338

African (AFR) AF: 0.294 AC: 12176 AN: 41468

American (AMR) AF: 0.229 AC: 3496 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 903 AN: 3470

East Asian (EAS) AF: 0.298 AC: 1537 AN: 5160

South Asian (SAS) AF: 0.275 AC: 1326 AN: 4820

European-Finnish (FIN) AF: 0.209 AC: 2210 AN: 10582

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14738 AN: 67960

Other (OTH) AF: 0.251 AC: 529 AN: 2110

Alfa AF: 0.209 Hom.: 2017

Bravo AF: 0.248

Asia WGS AF: 0.272 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	1.4
DANN	Benign	0.18
PhyloP100		2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1887027;

hg19: chr10-6113782;