5-17156347-A-G

Variant names:

• chr5-17156347-A-G
• rs297179
• ENST00000606445.1:c.-72-55773A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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:26609): (BASP1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BASP1-AS1	NR_027253.1	n.1443+6122T>C		intron_variant	Intron 2 of 2

Ensembl

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

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

African (AFR) AF: 0.416 AC: 13842 AN: 33288

American (AMR) AF: 0.648 AC: 7636 AN: 11786

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1758 AN: 3346

East Asian (EAS) AF: 0.491 AC: 2196 AN: 4470

South Asian (SAS) AF: 0.478 AC: 1833 AN: 3836

European-Finnish (FIN) AF: 0.638 AC: 4559 AN: 7144

Middle Eastern (MID) AF: 0.613 AC: 146 AN: 238

European-Non Finnish (NFE) AF: 0.569 AC: 36642 AN: 64422

Other (OTH) AF: 0.548 AC: 939 AN: 1714

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
PhyloP100		-2.5

Splicing

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

Other links and lift over

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