rs1438106

Positions:

• chr20-1678815-G-A
• chr20-1678815-G-C

Variant summary

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

The ENST00000340424.4(SIRPB3P):​n.461-7618C>T 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 0.243 in 152,044 control chromosomes in the GnomAD database, including 5,208 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 0.24 (5208 hom., cov: 32)
• Consequence: SIRPB3P ENST00000340424.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

Genes affected

SIRPB3P (HGNC:49209): (signal regulatory protein beta 3, pseudogene)

SIRPG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SIRPG	XM_011529286.3	c.-27+7517C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SIRPB3P	ENST00000340424.4	n.461-7618C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36970 AN: 151926 Hom.: 5206 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.243 AC: 36983 AN: 152044 Hom.: 5208 Cov.: 32 AF XY: 0.251 AC XY: 18615 AN XY: 74306

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.282

Alfa AF: 0.255 Hom.: 879

Bravo AF: 0.233

Asia WGS AF: 0.515 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1438106; hg19: chr20-1659461;