rs1438098

chr20-1701283-A-G

Variant summary

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

The NR_164369.1(SIRPB3P):n.254+349T>C 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 152,164 control chromosomes in the GnomAD database, including 2,853 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 (2853 hom., cov: 31)
• Consequence: SIRPB3P NR_164369.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SIRPB3P	NR_164369.1	n.254+349T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SIRPB3P	ENST00000340424.4	n.73-3504T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25531 AN: 152046 Hom.: 2851 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0941

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0414

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.168 AC: 25575 AN: 152164 Hom.: 2853 Cov.: 31 AF XY: 0.163 AC XY: 12123 AN XY: 74402

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.0940

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0414

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.138

Alfa AF: 0.159 Hom.: 338

Bravo AF: 0.171

Asia WGS AF: 0.0440 AC: 155 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	0.75
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1438098; hg19: chr20-1681929;