ENST00000606445.1:c.-73+59641A>G

Variant names:

• chr5-17148802-A-G
• rs682748
• ENST00000606445.1:c.-73+59641A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-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 rank	MANE	Protein	UniProt
BASP1-AS1	NR_027253.1	n.1443+13667T>C		intron_variant	Intron 2 of 2

Ensembl

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

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

African (AFR) AF: 0.387 AC: 16034 AN: 41452

American (AMR) AF: 0.605 AC: 9227 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1818 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2115 AN: 5170

South Asian (SAS) AF: 0.469 AC: 2263 AN: 4824

European-Finnish (FIN) AF: 0.595 AC: 6265 AN: 10536

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38335 AN: 67952

Other (OTH) AF: 0.523 AC: 1105 AN: 2112

Alfa AF: 0.537 Hom.: 50972

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs682748; hg19: chr5-17148911;