5-17215335-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606445.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BASP1-AS1	NR_027253.1		n.1346+742C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BASP1	ENST00000606445.1	TSL:3	c.-10+3153G>C		intron	N/A	ENSP00000476090.1	U3KQP0
	BASP1-AS1	ENST00000399760.2	TSL:2	n.971+742C>G		intron	N/A
	BASP1-AS1	ENST00000655365.1		n.721+742C>G		intron	N/A

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

African (AFR) AF: 0.748 AC: 31036 AN: 41472

American (AMR) AF: 0.732 AC: 11183 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2047 AN: 3468

East Asian (EAS) AF: 0.643 AC: 3326 AN: 5174

South Asian (SAS) AF: 0.601 AC: 2898 AN: 4824

European-Finnish (FIN) AF: 0.602 AC: 6355 AN: 10548

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43884 AN: 67996

Other (OTH) AF: 0.667 AC: 1405 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.49
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2962370; hg19: chr5-17215444;