20-1700963-A-T

Variant summary

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

The NR_164369.1(SIRPB3P):n.254+669T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 151,650 control chromosomes in the GnomAD database, including 2,836 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 0.17 (2836 hom., cov: 31)
• Consequence: SIRPB3P NR_164369.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

Genes affected

SIRPB3P (HGNC:49209): (signal regulatory protein beta 3, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SIRPB3P	NR_164369.1	n.254+669T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SIRPB3P	ENST00000340424.4	n.73-3184T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25379 AN: 151532 Hom.: 2832 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.0584

Gnomad AMR AF: 0.0983

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.000967

Gnomad SAS AF: 0.0409

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.168 AC: 25416 AN: 151650 Hom.: 2836 Cov.: 31 AF XY: 0.163 AC XY: 12071 AN XY: 74110

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.0981

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.000970

Gnomad4 SAS AF: 0.0409

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.139

Alfa AF: 0.0680 Hom.: 82

Bravo AF: 0.172

Asia WGS AF: 0.0420 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.8
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1438101; hg19: chr20-1681609;