5-17215335-G-C

Variant names:

• chr5-17215335-G-C
• rs2962370
• ENST00000606445.1:c.-10+3153G>C

Variant summary

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

The ENST00000606445.1(BASP1):​c.-10+3153G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,076 control chromosomes in the GnomAD database, including 34,987 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 0.68 (34987 hom., cov: 32)
• Consequence: BASP1 ENST00000606445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BASP1-AS1	NR_027253.1	n.1346+742C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BASP1	ENST00000606445.1	c.-10+3153G>C		intron_variant	Intron 3 of 3	3		ENSP00000476090.1
BASP1-AS1	ENST00000399760.2	n.971+742C>G		intron_variant	Intron 1 of 2	2
BASP1-AS1	ENST00000655365.1	n.721+742C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102765 AN: 151958 Hom.: 34953 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.676 AC: 102852 AN: 152076 Hom.: 34987 Cov.: 32 AF XY: 0.675 AC XY: 50155 AN XY: 74326

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.667

Alfa AF: 0.554 Hom.: 1506

Bravo AF: 0.692

Asia WGS AF: 0.648 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2962370; hg19: chr5-17215444;