chr16-46614446-G-A

Variant names:

• chr16-46614446-G-A
• rs17734120
• NM_024745.5:c.596+1500C>T

Variant summary

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

The NM_024745.5(SHCBP1):​c.596+1500C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,938 control chromosomes in the GnomAD database, including 10,506 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 0.33 (10506 hom., cov: 32)
• Consequence: SHCBP1 NM_024745.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 3 publications found

Genes affected

SHCBP1 (HGNC:29547): (SHC binding and spindle associated 1) Predicted to enable SH2 domain binding activity. Predicted to be involved in fibroblast growth factor receptor signaling pathway and regulation of neural precursor cell proliferation. Predicted to be located in cytoplasm; midbody; and spindle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024745.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHCBP1	NM_024745.5	MANE Select	c.596+1500C>T		intron	N/A	NP_079021.4
	SHCBP1	NM_001324318.2		c.482+1500C>T		intron	N/A	NP_001311247.1
	SHCBP1	NM_001324319.2		c.596+1500C>T		intron	N/A	NP_001311248.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHCBP1	ENST00000303383.8	TSL:1 MANE Select	c.596+1500C>T		intron	N/A	ENSP00000306473.3
	SHCBP1	ENST00000566016.5	TSL:1	n.605+1500C>T		intron	N/A
	SHCBP1	ENST00000569702.1	TSL:3	c.47+1500C>T		intron	N/A	ENSP00000460840.1

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50131 AN: 151818 Hom.: 10508 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.0425

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.330 AC: 50136 AN: 151938 Hom.: 10506 Cov.: 32 AF XY: 0.326 AC XY: 24198 AN XY: 74232

African (AFR) AF: 0.102 AC: 4234 AN: 41468

American (AMR) AF: 0.346 AC: 5278 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1549 AN: 3472

East Asian (EAS) AF: 0.0426 AC: 219 AN: 5144

South Asian (SAS) AF: 0.246 AC: 1183 AN: 4810

European-Finnish (FIN) AF: 0.402 AC: 4239 AN: 10534

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 31990 AN: 67934

Other (OTH) AF: 0.368 AC: 775 AN: 2104

Alfa AF: 0.410 Hom.: 2379

Bravo AF: 0.313

Asia WGS AF: 0.152 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.63
PhyloP100		-0.080
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs17734120; hg19: chr16-46648358;