rs6603859

Positions:

• chr1-16379580-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001114600.3(SZRD1):​c.52-11795G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 152,006 control chromosomes in the GnomAD database, including 19,729 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 0.51 (19729 hom., cov: 32)
• Consequence: SZRD1 NM_001114600.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

Genes affected

SZRD1 (HGNC:30232): (SUZ RNA binding domain containing 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SZRD1	NM_001114600.3	c.52-11795G>T		intron_variant		ENST00000401088.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SZRD1	ENST00000401088.9	c.52-11795G>T		intron_variant		1	NM_001114600.3	P4

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77353 AN: 151888 Hom.: 19715 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.509 AC: 77409 AN: 152006 Hom.: 19729 Cov.: 32 AF XY: 0.508 AC XY: 37769 AN XY: 74296

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.507

Alfa AF: 0.505 Hom.: 3710

Bravo AF: 0.504

Asia WGS AF: 0.513 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.6
DANN	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6603859; hg19: chr1-16706075;