chr5-17156347-A-G

Position:

• chr5-17156347-A-G

Variant summary

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

The ENST00000606445.1(BASP1):​c.-72-55773A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.53 (18724 hom., cov: 17)
• Consequence: BASP1 ENST00000606445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BASP1-AS1	NR_027253.1	n.1443+6122T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BASP1	ENST00000606445.1	c.-72-55773A>G		intron_variant		3		ENSP00000476090.1
BASP1-AS1	ENST00000399760.2	n.1068+6122T>C		intron_variant		2
BASP1-AS1	ENST00000655365.1	n.818+6122T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.534 AC: 70015 AN: 131036 Hom.: 18717 Cov.: 17

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.619

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.534 AC: 70048 AN: 131112 Hom.: 18724 Cov.: 17 AF XY: 0.537 AC XY: 33342 AN XY: 62056

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.548

Alfa AF: 0.362 Hom.: 841

Bravo AF: 0.515

Asia WGS AF: 0.451 AC: 1561 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs297179; hg19: chr5-17156456; COSMIC: COSV67659996;