rs6034368

Positions:

• chr20-1677612-C-T

Variant summary

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

The ENST00000340424.4(SIRPB3P):​n.461-6415G>A 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 0.245 in 152,060 control chromosomes in the GnomAD database, including 5,276 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 (5276 hom., cov: 32)
• Consequence: SIRPB3P ENST00000340424.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

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=-0.99).
• 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	Protein	UniProt
SIRPG	XM_011529286.3	c.-27+8720G>A		intron_variant			XP_011527588.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIRPB3P	ENST00000340424.4	n.461-6415G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37196 AN: 151942 Hom.: 5274 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.245 AC: 37209 AN: 152060 Hom.: 5276 Cov.: 32 AF XY: 0.252 AC XY: 18753 AN XY: 74340

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.283

Alfa AF: 0.261 Hom.: 2710

Bravo AF: 0.235

Asia WGS AF: 0.514 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6034368; hg19: chr20-1658258;