rs2929724

Positions:

• chr5-17200318-C-G

Variant summary

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

The NR_027253.1(BASP1-AS1):​n.1346+15759G>C variant causes a intron, non coding transcript 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-AS1 NR_027253.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

Genes affected

BASP1-AS1 (HGNC:26609): (BASP1 antisense RNA 1)

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
BASP1-AS1	NR_027253.1	n.1346+15759G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BASP1-AS1	ENST00000655365.1	n.721+15759G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.515

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2929724; hg19: chr5-17200427;