20-1698888-C-T

Position:

• chr20-1698888-C-T

Variant summary

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

The NR_164369.1(SIRPB3P):​n.255-1109G>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 NR_164369.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

Genes affected

SIRPB3P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SIRPB3P	NR_164369.1	n.255-1109G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIRPB3P	ENST00000340424.4	n.73-1109G>A		intron_variant		6

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

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.588

Alfa AF: 0.562 Hom.: 4567

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs202479; hg19: chr20-1679534;