rs682748

Positions:

• chr5-17148802-A-G

Variant summary

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

The ENST00000606445.1(BASP1):​c.-73+59641A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,982 control chromosomes in the GnomAD database, including 20,630 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 0.51 (20630 hom., cov: 32)
• Consequence: BASP1 ENST00000606445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

BASP1 (HGNC:957): (brain abundant membrane attached signal protein 1) This gene encodes a membrane bound protein with several transient phosphorylation sites and PEST motifs. Conservation of proteins with PEST sequences among different species supports their functional significance. PEST sequences typically occur in proteins with high turnover rates. Immunological characteristics of this protein are species specific. This protein also undergoes N-terminal myristoylation. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Oct 2012]

BASP1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BASP1-AS1	NR_027253.1	n.1443+13667T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BASP1	ENST00000606445.1	c.-73+59641A>G		intron_variant		3		ENSP00000476090.1
BASP1-AS1	ENST00000399760.2	n.1068+13667T>C		intron_variant		2
BASP1-AS1	ENST00000655365.1	n.818+13667T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77793 AN: 151864 Hom.: 20615 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.512 AC: 77848 AN: 151982 Hom.: 20630 Cov.: 32 AF XY: 0.513 AC XY: 38125 AN XY: 74312

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.523

Alfa AF: 0.547 Hom.: 32168

Bravo AF: 0.510

Asia WGS AF: 0.418 AC: 1450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.32
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs682748; hg19: chr5-17148911;