rs10420134

Variant names:

• chr19-35771026-A-G
• rs10420134
• NM_001367856.1:c.*2481A>G

Variant summary

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

The NM_001367856.1(PROSER3):​c.*2481A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,044 control chromosomes in the GnomAD database, including 3,920 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 0.22 (3920 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: PROSER3 NM_001367856.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 9 publications found

Genes affected

PROSER3 (HGNC:25204): (proline and serine rich 3)

ENSG00000267049 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367856.1. 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
	PROSER3	NM_001367856.1	MANE Select	c.*2481A>G		3_prime_UTR	Exon 11 of 11	NP_001354785.1
	PROSER3	NM_001438802.1		c.*2481A>G		3_prime_UTR	Exon 11 of 11	NP_001425731.1
	PROSER3	NM_001395458.1		c.*2286A>G		3_prime_UTR	Exon 12 of 12	NP_001382387.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PROSER3	ENST00000646935.2	MANE Select	c.*2481A>G		3_prime_UTR	Exon 11 of 11	ENSP00000496769.2
	PROSER3	ENST00000396908.10	TSL:1	c.*2481A>G		3_prime_UTR	Exon 11 of 11	ENSP00000380116.5
	PROSER3	ENST00000544158.2	TSL:5	n.1072A>G		splice_region non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33559 AN: 151920 Hom.: 3920 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.216

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.221 AC: 33582 AN: 152038 Hom.: 3920 Cov.: 32 AF XY: 0.226 AC XY: 16809 AN XY: 74322

African (AFR) AF: 0.268 AC: 11114 AN: 41448

American (AMR) AF: 0.256 AC: 3902 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3472

East Asian (EAS) AF: 0.421 AC: 2176 AN: 5166

South Asian (SAS) AF: 0.217 AC: 1049 AN: 4824

European-Finnish (FIN) AF: 0.200 AC: 2116 AN: 10578

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.174 AC: 11856 AN: 67990

Other (OTH) AF: 0.214 AC: 451 AN: 2110

Alfa AF: 0.192 Hom.: 8258

Bravo AF: 0.233

Asia WGS AF: 0.270 AC: 939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.38
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs10420134; hg19: chr19-36261928;