5-17116112-C-T

Variant names:

• chr5-17116112-C-T
• rs1351583
• ENST00000606445.1:c.-73+26951C>T

Variant summary

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

The ENST00000606445.1(BASP1):​c.-73+26951C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,130 control chromosomes in the GnomAD database, including 7,264 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 0.29 (7264 hom., cov: 32)
• Consequence: BASP1 ENST00000606445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

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)

LOC124900947 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900947	XR_007058707.1	n.126+1249G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BASP1	ENST00000606445.1	c.-73+26951C>T		intron_variant	Intron 2 of 3	3		ENSP00000476090.1
BASP1-AS1	ENST00000655365.1	n.819-25804G>A		intron_variant	Intron 2 of 2
BASP1-AS1	ENST00000661332.1	n.204-8802G>A		intron_variant	Intron 2 of 2
BASP1-AS1	ENST00000668327.1	n.816-12208G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43497 AN: 152012 Hom.: 7262 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.286 AC: 43507 AN: 152130 Hom.: 7264 Cov.: 32 AF XY: 0.288 AC XY: 21420 AN XY: 74386

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.317

Alfa AF: 0.349 Hom.: 8674

Bravo AF: 0.275

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1351583; hg19: chr5-17116221;