20-1490964-C-T

Position:

• chr20-1490964-C-T

Variant summary

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

The NM_001122962.2(SIRPB2):​c.85+311G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,152 control chromosomes in the GnomAD database, including 3,491 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 0.16 (3491 hom., cov: 32)
• Consequence: SIRPB2 NM_001122962.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

Genes affected

SIRPB2 (HGNC:16247): (signal regulatory protein beta 2) Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SIRPB2	NM_001122962.2	c.85+311G>A		intron_variant		ENST00000359801.8	NP_001116434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIRPB2	ENST00000359801.8	c.85+311G>A		intron_variant		2	NM_001122962.2	ENSP00000352849	P1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24199 AN: 152034 Hom.: 3489 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0899

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0546

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.159 AC: 24229 AN: 152152 Hom.: 3491 Cov.: 32 AF XY: 0.155 AC XY: 11508 AN XY: 74396

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.0896

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0546

Gnomad4 NFE AF: 0.0734

Gnomad4 OTH AF: 0.135

Alfa AF: 0.106 Hom.: 834

Bravo AF: 0.171

Asia WGS AF: 0.0770 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.8
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6110193; hg19: chr20-1471610;