rs1347741

Variant names:

• chr20-1718317-G-A
• rs1347741
• ENST00000844954.1:n.699+3853C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-1718317-G-A
• chr20-1718317-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000844954.1(ENSG00000286288):​n.699+3853C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00941 in 152,164 control chromosomes in the GnomAD database, including 24 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 0.0094 (24 hom., cov: 32)
• Consequence: ENSG00000286288 ENST00000844954.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.917
• Publications: 0 publications found

Genes affected

ENSG00000286288 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00941 (1432/152164) while in subpopulation AFR AF = 0.0322 (1336/41520). AF 95% confidence interval is 0.0307. There are 24 homozygotes in GnomAd4. There are 672 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 24 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SIRPB3P	NR_164369.1	n.123+3853C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286288	ENST00000844954.1	n.699+3853C>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.00937 AC: 1425 AN: 152046 Hom.: 24 Cov.: 32

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00393

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000883

Gnomad OTH AF: 0.00908

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

GnomAD4 genome AF: 0.00941 AC: 1432 AN: 152164 Hom.: 24 Cov.: 32 AF XY: 0.00903 AC XY: 672 AN XY: 74396

African (AFR) AF: 0.0322 AC: 1336 AN: 41520

American (AMR) AF: 0.00392 AC: 60 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00 AC: 0 AN: 4808

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10608

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000883 AC: 6 AN: 67968

Other (OTH) AF: 0.00899 AC: 19 AN: 2114

Alfa AF: 0.00193 Hom.: 2

Bravo AF: 0.0112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.30
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs1347741; hg19: chr20-1698963;