5-17070596-A-G

Variant summary

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

The ENST00000606445.1(BASP1):c.-162+4896A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0946 in 152,280 control chromosomes in the GnomAD database, including 909 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 0.095 (909 hom., cov: 32)
• Consequence: BASP1 ENST00000606445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BASP1	ENST00000606445.1	c.-162+4896A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0947 AC: 14407 AN: 152162 Hom.: 907 Cov.: 32

Gnomad AFR AF: 0.0286

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0893

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

GnomAD4 genome AF: 0.0946 AC: 14406 AN: 152280 Hom.: 909 Cov.: 32 AF XY: 0.0965 AC XY: 7187 AN XY: 74446

Gnomad4 AFR AF: 0.0285

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0533

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.0884

Alfa AF: 0.0896 Hom.: 231

Bravo AF: 0.0910

Asia WGS AF: 0.103 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	0.39
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17542943; hg19: chr5-17070705;