rs2088578

Variant names:

• chr12-68804332-G-A
• rs2088578
• NR_073494.1:n.*105C>T

Variant summary

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

The NR_073494.1(SZRD1P1):​n.*105C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,040 control chromosomes in the GnomAD database, including 26,875 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 0.56 (26875 hom., cov: 32)
• Consequence: SZRD1P1 NR_073494.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 6 publications found

Genes affected

SZRD1P1 (HGNC:56315): (SZRD1 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SZRD1P1	NR_073494.1	n.*105C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85137 AN: 151922 Hom.: 26816 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.508

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.561 AC: 85263 AN: 152040 Hom.: 26875 Cov.: 32 AF XY: 0.550 AC XY: 40853 AN XY: 74310

African (AFR) AF: 0.863 AC: 35779 AN: 41476

American (AMR) AF: 0.373 AC: 5691 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1268 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1459 AN: 5146

South Asian (SAS) AF: 0.312 AC: 1505 AN: 4820

European-Finnish (FIN) AF: 0.456 AC: 4826 AN: 10576

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33048 AN: 67974

Other (OTH) AF: 0.507 AC: 1068 AN: 2106

Alfa AF: 0.508 Hom.: 56395

Bravo AF: 0.570

Asia WGS AF: 0.360 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.62
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2088578; hg19: chr12-69198112;