rs6110193

Variant names:

• chr20-1490964-C-T
• rs6110193
• NM_001122962.2:c.85+311G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001122962.2. 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
	SIRPB2	NM_001122962.2	MANE Select	c.85+311G>A		intron	N/A	NP_001116434.1	Q5JXA9-1
	SIRPB2	NM_001134836.2		c.85+311G>A		intron	N/A	NP_001128308.1	Q5JXA9-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIRPB2	ENST00000359801.8	TSL:2 MANE Select	c.85+311G>A		intron	N/A	ENSP00000352849.3	Q5JXA9-1
	SIRPB2	ENST00000381630.2	TSL:1	n.109+311G>A		intron	N/A
	SIRPB2	ENST00000444444.2	TSL:2	c.85+311G>A		intron	N/A	ENSP00000402438.1	Q5JXA9-3

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

African (AFR) AF: 0.384 AC: 15926 AN: 41464

American (AMR) AF: 0.0896 AC: 1370 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 392 AN: 3468

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5192

South Asian (SAS) AF: 0.124 AC: 596 AN: 4814

European-Finnish (FIN) AF: 0.0546 AC: 580 AN: 10614

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0734 AC: 4993 AN: 67998

Other (OTH) AF: 0.135 AC: 285 AN: 2114

Alfa AF: 0.107 Hom.: 932

Bravo AF: 0.171

Asia WGS AF: 0.0770 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.8
DANN	Benign	0.43
PhyloP100		0.35
PromoterAI		-0.036	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6110193; hg19: chr20-1471610;