rs12412095

Variant names:

• chr10-6071560-A-G
• rs12412095
• ENST00000397237.2:n.359T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-6071560-A-G
• chr10-6071560-A-T

Variant summary

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

The ENST00000397237.2(RPL32P23):​n.359T>C 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 0.255 in 152,776 control chromosomes in the GnomAD database, including 5,672 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 0.26 (5639 hom., cov: 31)
  • Exomes 𝑓: 0.25 (33 hom.)
• Consequence: RPL32P23 ENST00000397237.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.56
• Publications: 11 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=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL32P23		n.6071560A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL32P23	ENST00000397237.2	n.359T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38660 AN: 151546 Hom.: 5629 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.247

GnomAD4 exome AF: 0.251 AC: 279 AN: 1110 Hom.: 33 Cov.: 0 AF XY: 0.265 AC XY: 179 AN XY: 676

African (AFR) AF: 0.107 AC: 3 AN: 28

American (AMR) AF: 0.0946 AC: 7 AN: 74

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18

East Asian (EAS) AF: 0.145 AC: 11 AN: 76

South Asian (SAS) AF: 0.212 AC: 17 AN: 80

European-Finnish (FIN) AF: 0.290 AC: 47 AN: 162

Middle Eastern (MID) AF: 0.250 AC: 1 AN: 4

European-Non Finnish (NFE) AF: 0.298 AC: 177 AN: 594

Other (OTH) AF: 0.216 AC: 16 AN: 74

GnomAD4 genome AF: 0.255 AC: 38683 AN: 151666 Hom.: 5639 Cov.: 31 AF XY: 0.257 AC XY: 19044 AN XY: 74124

African (AFR) AF: 0.132 AC: 5454 AN: 41186

American (AMR) AF: 0.223 AC: 3406 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1376 AN: 5156

South Asian (SAS) AF: 0.330 AC: 1587 AN: 4806

European-Finnish (FIN) AF: 0.360 AC: 3803 AN: 10550

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21483 AN: 67930

Other (OTH) AF: 0.250 AC: 527 AN: 2112

Alfa AF: 0.272 Hom.: 6090

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs12412095; hg19: chr10-6113523;