5-17116112-C-T

Variant names:

• chr5-17116112-C-T
• rs1351583
• ENST00000606445.1:c.-73+26951C>T

Variant summary

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

The ENST00000606445.1(BASP1):​c.-73+26951C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,130 control chromosomes in the GnomAD database, including 7,264 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 0.29 (7264 hom., cov: 32)
• Consequence: BASP1 ENST00000606445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 1 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)

LOC124900947 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.36 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BASP1	ENST00000606445.1	TSL:3	c.-73+26951C>T		intron	N/A	ENSP00000476090.1	U3KQP0
	BASP1-AS1	ENST00000655365.1		n.819-25804G>A		intron	N/A
	BASP1-AS1	ENST00000661332.1		n.204-8802G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43497 AN: 152012 Hom.: 7262 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.286 AC: 43507 AN: 152130 Hom.: 7264 Cov.: 32 AF XY: 0.288 AC XY: 21420 AN XY: 74386

African (AFR) AF: 0.104 AC: 4314 AN: 41524

American (AMR) AF: 0.347 AC: 5301 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1060 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1173 AN: 5166

South Asian (SAS) AF: 0.302 AC: 1455 AN: 4822

European-Finnish (FIN) AF: 0.418 AC: 4421 AN: 10576

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24739 AN: 67972

Other (OTH) AF: 0.317 AC: 669 AN: 2112

Alfa AF: 0.340 Hom.: 11073

Bravo AF: 0.275

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.1
DANN	Benign	0.70
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs1351583; hg19: chr5-17116221;