20-1698888-C-T

Variant names:

• chr20-1698888-C-T
• rs202479
• ENST00000340424.4:n.73-1109G>A

Variant summary

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

The ENST00000340424.4(SIRPB3P):​n.73-1109G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,730 control chromosomes in the GnomAD database, including 25,833 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 0.57 (25833 hom., cov: 30)
• Consequence: SIRPB3P ENST00000340424.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SIRPB3P	NR_164369.1	n.255-1109G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SIRPB3P	ENST00000340424.4	n.73-1109G>A		intron_variant	Intron 1 of 4	6
ENSG00000286288	ENST00000844954.1	n.700-1109G>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85717 AN: 151612 Hom.: 25824 Cov.: 30

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.565 AC: 85774 AN: 151730 Hom.: 25833 Cov.: 30 AF XY: 0.570 AC XY: 42270 AN XY: 74130

African (AFR) AF: 0.374 AC: 15467 AN: 41302

American (AMR) AF: 0.684 AC: 10446 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2077 AN: 3464

East Asian (EAS) AF: 0.959 AC: 4964 AN: 5174

South Asian (SAS) AF: 0.817 AC: 3926 AN: 4806

European-Finnish (FIN) AF: 0.544 AC: 5710 AN: 10502

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41179 AN: 67910

Other (OTH) AF: 0.588 AC: 1237 AN: 2102

Alfa AF: 0.557 Hom.: 4628

Bravo AF: 0.566

Asia WGS AF: 0.856 AC: 2975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.62
DANN	Benign	0.24
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs202479; hg19: chr20-1679534;