chr20-1700963-A-T

Variant names:

• chr20-1700963-A-T
• rs1438101
• ENST00000340424.4:n.73-3184T>A

Variant summary

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

The NR_164369.1(SIRPB3P):​n.254+669T>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 1 publications found

Genes affected

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

ENSG00000286288 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_164369.1. 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
	SIRPB3P	NR_164369.1		n.254+669T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIRPB3P	ENST00000340424.4	TSL:6	n.73-3184T>A		intron	N/A
	ENSG00000286288	ENST00000844954.1		n.700-3184T>A		intron	N/A

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

African (AFR) AF: 0.318 AC: 13138 AN: 41252

American (AMR) AF: 0.0981 AC: 1495 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3466

East Asian (EAS) AF: 0.000970 AC: 5 AN: 5156

South Asian (SAS) AF: 0.0409 AC: 196 AN: 4790

European-Finnish (FIN) AF: 0.116 AC: 1218 AN: 10508

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8497 AN: 67930

Other (OTH) AF: 0.139 AC: 293 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.31
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1438101; hg19: chr20-1681609;