rs2929724

Variant names:

• chr5-17200318-C-G
• rs2929724
• ENST00000606445.1:c.-72-11802C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000606445.1(BASP1):​c.-72-11802C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,916 control chromosomes in the GnomAD database, including 20,196 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 (20196 hom., cov: 32)
• Consequence: BASP1 ENST00000606445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BASP1-AS1	NR_027253.1	n.1346+15759G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BASP1	ENST00000606445.1	c.-72-11802C>G		intron_variant	Intron 2 of 3	3		ENSP00000476090.1
BASP1-AS1	ENST00000399760.2	n.971+15759G>C		intron_variant	Intron 1 of 2	2
BASP1-AS1	ENST00000655365.1	n.721+15759G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77534 AN: 151798 Hom.: 20179 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.511 AC: 77592 AN: 151916 Hom.: 20196 Cov.: 32 AF XY: 0.516 AC XY: 38320 AN XY: 74258

African (AFR) AF: 0.454 AC: 18769 AN: 41384

American (AMR) AF: 0.569 AC: 8690 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1637 AN: 3468

East Asian (EAS) AF: 0.454 AC: 2337 AN: 5148

South Asian (SAS) AF: 0.467 AC: 2252 AN: 4824

European-Finnish (FIN) AF: 0.632 AC: 6685 AN: 10570

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.523 AC: 35544 AN: 67954

Other (OTH) AF: 0.515 AC: 1083 AN: 2102

Alfa AF: 0.516 Hom.: 2534

Bravo AF: 0.508

Asia WGS AF: 0.479 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2929724; hg19: chr5-17200427;